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- PDB-6nzy: Structural Determination of the Carboxy-terminal portion of ATP-c... -

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Basic information

Entry
Database: PDB / ID: 6nzy
TitleStructural Determination of the Carboxy-terminal portion of ATP-citrate lyase
ComponentsATP-citrate lyase alpha-subunit
KeywordsLYASE / Carboxy-terminal portion / acetyl-CoA / acyl-CoA synthetase
Function / homology
Function and homology information


acyltransferase activity, acyl groups converted into alkyl on transfer / citrate synthase (unknown stereospecificity) / tricarboxylic acid cycle / lipid metabolic process / lyase activity / ATP binding / cytoplasm
Similarity search - Function
ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / Citrate synthase-like, large alpha subdomain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily ...ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / Citrate synthase-like, large alpha subdomain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / PHOSPHATE ION / citrate synthase (unknown stereospecificity)
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNguyen, V.H. / Fraser, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)222915-2013 Canada
CitationJournal: Protein Sci. / Year: 2019
Title: Identification of the active site residues in ATP-citrate lyase's carboxy-terminal portion.
Authors: Nguyen, V.H. / Singh, N. / Medina, A. / Uson, I. / Fraser, M.E.
History
DepositionFeb 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-citrate lyase alpha-subunit
B: ATP-citrate lyase alpha-subunit
C: ATP-citrate lyase alpha-subunit
D: ATP-citrate lyase alpha-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,87732
Polymers115,4054
Non-polymers3,47228
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34610 Å2
ΔGint-321 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.180, 82.180, 151.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 354 through 355 or resid 358...
21(chain B and (resid 354 through 355 or resid 358...
31(chain C and (resid 354 through 355 or resid 358...
41(chain D and (resid 354 through 355 or resid 358...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 354 through 355 or resid 358...A354 - 355
121(chain A and (resid 354 through 355 or resid 358...A358 - 424
131(chain A and (resid 354 through 355 or resid 358...A426
141(chain A and (resid 354 through 355 or resid 358...A428 - 433
151(chain A and (resid 354 through 355 or resid 358...A435 - 439
161(chain A and (resid 354 through 355 or resid 358...A441 - 496
171(chain A and (resid 354 through 355 or resid 358...A498 - 509
181(chain A and (resid 354 through 355 or resid 358...A512 - 515
191(chain A and (resid 354 through 355 or resid 358...A517 - 533
1101(chain A and (resid 354 through 355 or resid 358...A535 - 587
1111(chain A and (resid 354 through 355 or resid 358...A589 - 606
211(chain B and (resid 354 through 355 or resid 358...B354 - 355
221(chain B and (resid 354 through 355 or resid 358...B358 - 424
231(chain B and (resid 354 through 355 or resid 358...B426
241(chain B and (resid 354 through 355 or resid 358...B428 - 433
251(chain B and (resid 354 through 355 or resid 358...B435 - 439
261(chain B and (resid 354 through 355 or resid 358...B441 - 496
271(chain B and (resid 354 through 355 or resid 358...B498 - 509
281(chain B and (resid 354 through 355 or resid 358...B512 - 515
291(chain B and (resid 354 through 355 or resid 358...B517 - 533
2101(chain B and (resid 354 through 355 or resid 358...B535 - 587
2111(chain B and (resid 354 through 355 or resid 358...B589 - 606
311(chain C and (resid 354 through 355 or resid 358...C354 - 355
321(chain C and (resid 354 through 355 or resid 358...C358 - 424
331(chain C and (resid 354 through 355 or resid 358...C351 - 607
341(chain C and (resid 354 through 355 or resid 358...C435
351(chain C and (resid 354 through 355 or resid 358...C9
361(chain C and (resid 354 through 355 or resid 358...C498 - 509
371(chain C and (resid 354 through 355 or resid 358...C512 - 515
381(chain C and (resid 354 through 355 or resid 358...C517
391(chain C and (resid 354 through 355 or resid 358...C57
3101(chain C and (resid 354 through 355 or resid 358...C589 - 606
411(chain D and (resid 354 through 355 or resid 358...D354 - 355
421(chain D and (resid 354 through 355 or resid 358...D358 - 424
431(chain D and (resid 354 through 355 or resid 358...D426
441(chain D and (resid 354 through 355 or resid 358...D441 - 496
451(chain D and (resid 354 through 355 or resid 358...D498 - 509
461(chain D and (resid 354 through 355 or resid 358...D512 - 51
471(chain D and (resid 354 through 355 or resid 358...D517 - 533
481(chain D and (resid 354 through 355 or resid 358...D535 - 587
491(chain D and (resid 354 through 355 or resid 358...D589 - 606

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ATP-citrate lyase alpha-subunit


Mass: 28851.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium limicola (bacteria) / Gene: aclA / Plasmid: pET42b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9AJC4

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Non-polymers , 5 types, 336 molecules

#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: PEG 3350, sodium acetate, MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.89→75.61 Å / Num. obs: 91455 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.89-1.943.80.61.91100
8.45-75.615.10.0261100

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Processing

Software
NameVersionClassification
PHENIXdev_3381refinement
DIALSdata reduction
DIALSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H12

2h12


Resolution: 1.9→71.17 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.71
RfactorNum. reflection% reflection
Rfree0.1896 4287 5.06 %
Rwork0.1666 --
obs0.1678 84682 94.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.45 Å2 / Biso mean: 57.2444 Å2 / Biso min: 20.15 Å2
Refinement stepCycle: final / Resolution: 1.9→71.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8002 0 332 308 8642
Biso mean--82.43 45.25 -
Num. residues----1035
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4526X-RAY DIFFRACTION5.456TORSIONAL
12B4526X-RAY DIFFRACTION5.456TORSIONAL
13C4526X-RAY DIFFRACTION5.456TORSIONAL
14D4526X-RAY DIFFRACTION5.456TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.35681170.32222215233277
1.9216-1.94420.33161170.29532245236279
1.9442-1.9680.24671200.27512286240681
1.968-1.99290.26341250.2482418254384
1.9929-2.01910.24261330.22762467260087
2.0191-2.04680.22831350.22172560269588
2.0468-2.0760.2411340.22122493262789
2.076-2.1070.24361400.21062594273490
2.107-2.13990.23651450.20232585273092
2.1399-2.1750.24881250.1922677280293
2.175-2.21250.20921460.18592672281894
2.2125-2.25270.21871460.18372677282394
2.2527-2.29610.22121500.17852725287595
2.2961-2.34290.21351470.17452691283895
2.3429-2.39390.19091430.1692714285796
2.3939-2.44960.18481370.1582785292297
2.4496-2.51080.1831520.15542752290497
2.5108-2.57870.1771510.15992826297798
2.5787-2.65460.17741450.162832297798
2.6546-2.74030.19741540.15682794294899
2.7403-2.83820.19351570.15152835299299
2.8382-2.95190.1611780.1472750292899
2.9519-3.08620.16621660.152128423008100
3.0862-3.24890.1891580.153728463004100
3.2489-3.45250.17561380.150428562994100
3.4525-3.71910.16781450.149828553000100
3.7191-4.09330.15451310.144728793010100
4.0933-4.68550.16851490.141228122961100
4.6855-5.90280.2141490.175428843033100
5.9028-71.21990.181540.180128282982100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.24340.2464-0.14611.2127-1.06922.4092-0.00060.08060.138-0.0092-0.05330.0399-0.16660.2610.06420.2021-0.0215-0.02010.2419-0.00160.257859.011367.75253.3282
23.7662-0.5239-0.25543.87010.613.0617-0.1232-0.54850.49550.4333-0.031.004-0.7013-0.46810.19580.67720.04080.10140.4528-0.14650.711349.731182.433475.9655
31.96470.15950.31063.37870.52822.1715-0.098-0.27380.45840.3497-0.03870.3244-0.62010.28210.08940.4433-0.0889-0.01440.3329-0.04630.371960.070575.374369.7357
45.84411.6383-0.89432.55730.09673.49260.0295-0.7981-0.68250.0841-0.1486-0.15670.46190.00020.06620.4024-0.03320.02570.22350.09650.341636.860242.371275.7152
55.68481.4151-0.76662.8684-0.60442.3689-0.18640.7291-0.117-0.44330.33060.19110.3671-0.5337-0.16720.4405-0.1806-0.11340.5445-0.00840.343328.043647.312641.1848
61.5530.8415-0.27792.1389-0.30861.6682-0.11480.0213-0.1599-0.26240.13990.16050.3504-0.2058-0.02890.2534-0.0445-0.00990.2064-0.00310.25838.160646.056662.4941
73.265-0.6268-0.5893.1802-0.36621.9748-0.25390.0708-0.7527-0.80350.0189-1.5210.88710.72020.12880.8310.02330.26410.5213-0.05351.300348.277523.98859.5625
81.60030.8587-0.8391.4318-0.55631.6549-0.39230.1532-0.6593-0.56590.2731-0.36990.8271-0.2021-0.05820.6406-0.13380.09320.2214-0.07080.503236.850931.634160.3226
99.20091.1729-0.09112.171-0.22841.94080.1428-1.31040.40120.2536-0.1083-0.0903-0.25790.3623-0.03910.3849-0.0355-0.06210.4689-0.06080.304160.735858.153577.0136
106.65032.5756-0.17249.1527-0.01033.4250.2579-0.6639-0.3540.7364-0.1741-0.14760.03070.2607-0.06830.2889-0.0089-0.09840.49820.09530.29964.654156.435676.0674
113.97911.1661-0.66582.2687-0.10853.67390.1484-0.1457-0.26210.1753-0.1109-0.49120.02160.8374-0.07130.222-0.0253-0.0170.53150.04130.356773.278263.445565.2334
127.6579-1.48842.27264.3759-0.7690.7247-0.1611-0.15250.1405-0.0552-0.1653-0.52450.08671.06290.32760.2427-0.0145-0.00280.63960.0830.32774.974664.079452.8407
133.0805-0.2586-0.1341.2042-0.89243.02470.00960.2082-0.0266-0.07820.02570.03990.14290.0303-0.02370.2364-0.0175-0.02060.2557-0.00040.2750.916661.783149
143.025-1.9038-1.63023.76232.37681.61620.60040.3755-1.0417-0.7108-0.55121.02041.37730.06010.50180.99350.3701-0.1220.7357-0.22720.799872.444140.925241.5892
154.8881-0.7422-1.16365.3317-3.89276.81270.49530.77920.0777-1.4903-0.30750.91711.0711-0.0236-0.15150.86340.2206-0.15580.6422-0.150.571267.17854.791832.5372
165.9717-1.63381.51825.3307-0.80761.06230.02630.0891-0.1548-0.4694-0.7223-0.88340.40890.79990.60030.43230.20850.09281.01330.14410.541479.863261.405843.6289
170.78682.03130.25296.0326-0.53351.8027-0.0806-0.018-0.4908-1.7243-0.3965-0.08870.72160.67670.34250.98210.54430.0610.8953-0.01540.519277.295249.104335.4391
182.94531.7857-2.18013.85080.34362.62860.34560.0705-0.0763-1.0359-0.65530.72740.18970.48130.43870.53780.2847-0.1360.6838-0.14950.523971.893753.236143.6427
194.9873-0.40920.01272.6919-0.44833.467-0.15160.234-0.2455-0.00920.11510.1192-0.04280.20760.0430.1906-0.04590.00110.2534-0.01040.21657.143364.258651.639
204.21613.2360.45913.82720.27051.9459-0.40090.71410.4772-0.47740.52360.59040.0668-0.4179-0.07450.4398-0.1246-0.09190.69010.06290.460631.013155.471837.5649
218.20233.4822.32265.1833.18355.87630.2059-0.5901-0.090.2908-0.10930.16350.5087-0.1768-0.11760.315-0.02520.06630.33570.05170.255835.71344.943877.6279
221.59680.6845-0.56311.0568-0.91232.2176-0.04660.16330.0701-0.09770.2540.24350.1386-0.4738-0.20560.2633-0.0624-0.03870.30880.03530.310630.532649.947956.274
232.21070.1236-0.40642.4869-0.66462.99770.12510.35620.9311-0.09810.43920.3592-0.7637-0.7119-0.32920.4970.13130.07280.71650.33440.920316.096466.578654.8688
242.1571.6008-1.09722.1801-1.28332.2329-0.1460.30310.052-0.23880.1901-0.00750.1965-0.1177-0.03430.2763-0.0097-0.04860.3168-0.00030.293246.126860.009744.0976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 347 through 451 )A347 - 451
2X-RAY DIFFRACTION2chain 'A' and (resid 452 through 500 )A452 - 500
3X-RAY DIFFRACTION3chain 'A' and (resid 501 through 582 )A501 - 582
4X-RAY DIFFRACTION4chain 'A' and (resid 583 through 608 )A583 - 608
5X-RAY DIFFRACTION5chain 'B' and (resid 350 through 398 )B350 - 398
6X-RAY DIFFRACTION6chain 'B' and (resid 399 through 451 )B399 - 451
7X-RAY DIFFRACTION7chain 'B' and (resid 452 through 500 )B452 - 500
8X-RAY DIFFRACTION8chain 'B' and (resid 501 through 581 )B501 - 581
9X-RAY DIFFRACTION9chain 'B' and (resid 582 through 607 )B582 - 607
10X-RAY DIFFRACTION10chain 'C' and (resid 351 through 373 )C351 - 373
11X-RAY DIFFRACTION11chain 'C' and (resid 374 through 398 )C374 - 398
12X-RAY DIFFRACTION12chain 'C' and (resid 399 through 411 )C399 - 411
13X-RAY DIFFRACTION13chain 'C' and (resid 412 through 451 )C412 - 451
14X-RAY DIFFRACTION14chain 'C' and (resid 452 through 482 )C452 - 482
15X-RAY DIFFRACTION15chain 'C' and (resid 483 through 500 )C483 - 500
16X-RAY DIFFRACTION16chain 'C' and (resid 501 through 518 )C501 - 518
17X-RAY DIFFRACTION17chain 'C' and (resid 519 through 534 )C519 - 534
18X-RAY DIFFRACTION18chain 'C' and (resid 535 through 556 )C535 - 556
19X-RAY DIFFRACTION19chain 'C' and (resid 557 through 582 )C557 - 582
20X-RAY DIFFRACTION20chain 'C' and (resid 583 through 607 )C583 - 607
21X-RAY DIFFRACTION21chain 'D' and (resid 350 through 373 )D350 - 373
22X-RAY DIFFRACTION22chain 'D' and (resid 374 through 451 )D374 - 451
23X-RAY DIFFRACTION23chain 'D' and (resid 452 through 556 )D452 - 556
24X-RAY DIFFRACTION24chain 'D' and (resid 557 through 607 )D557 - 607

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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