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- PDB-6c9e: Crystal structure of Cysteine desulfurase from Legionella pneumop... -

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Basic information

Entry
Database: PDB / ID: 6c9e
TitleCrystal structure of Cysteine desulfurase from Legionella pneumophila Philadelphia 1
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / transaminase activity / pyridoxal phosphate binding / lyase activity
Similarity search - Function
Cysteine desulfurase, SufS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...Cysteine desulfurase, SufS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cysteine desulfurase
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Cysteine desulfurase from Legionella pneumophila Philadelphia 1
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJan 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine desulfurase
B: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7738
Polymers94,3942
Non-polymers3796
Water21,2221178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-98 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.400, 71.150, 113.470
Angle α, β, γ (deg.)90.000, 102.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cysteine desulfurase /


Mass: 47196.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0604 / Plasmid: LepnA.01104.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q5ZXX6, cysteine desulfurase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1178 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: RigakuReagents JCSG+ B4: 10% PEG 8000, 8% Ethylene glycol, 100Mm HEPES free acid/NaOH pH 7.5: LepnA.01104.a.B1.PS38388 at 21.26mg/ml + 3mM Alanine: cryo: 15% EG: tray297375 b4: puck ugh2-4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→44.689 Å / Num. obs: 136069 / % possible obs: 99.9 % / Redundancy: 11.418 % / Biso Wilson estimate: 12.71 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.06 / Χ2: 1.069 / Net I/σ(I): 25.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.593.9640.4432.6299920.8050.5199.8
1.59-1.637.0750.3934.1698030.9190.42599.9
1.63-1.687.8960.3544.9694820.9470.378100
1.68-1.738.2560.315.8892530.960.33199.9
1.73-1.798.6690.2577.1889200.9750.273100
1.79-1.859.0240.2089.1586260.9860.22100
1.85-1.929.4730.17811.3284100.9890.188100
1.92-29.8940.14114.5280320.9940.149100
2-2.0910.3070.11418.7477580.9960.1299.9
2.09-2.1910.7480.09123.8973560.9980.096100
2.19-2.3111.8790.0929.1370380.9980.09499.8
2.31-2.4513.5430.07334.8166540.9990.07699.9
2.45-2.6214.3310.06440.7662650.9990.066100
2.62-2.8315.3820.05846.458210.9990.0699.9
2.83-3.116.9890.04956.1253850.9990.05100
3.1-3.4720.7290.04469.01485710.04599.9
3.47-422.1030.03980.97433110.04100
4-4.922.2510.03389.17363210.03499.8
4.9-6.9322.4240.03681.05284310.03699.9
6.93-44.68921.5010.02792.47161110.02899.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5j8q as per Morda

5j8q


Resolution: 1.55→44.689 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.38
RfactorNum. reflection% reflection
Rfree0.1637 2104 1.55 %
Rwork0.1403 --
obs0.1406 136055 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.1 Å2 / Biso mean: 17.6597 Å2 / Biso min: 6.48 Å2
Refinement stepCycle: final / Resolution: 1.55→44.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6315 0 18 1204 7537
Biso mean--33.57 31.37 -
Num. residues----811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.55-1.58610.23151320.20788849016
1.5861-1.62570.20671400.170688609000
1.6257-1.66970.19411360.15589119047
1.6697-1.71880.17051480.149589029050
1.7188-1.77430.16411150.149289299044
1.7743-1.83770.16821140.14689069020
1.8377-1.91130.16451670.151488799046
1.9113-1.99830.15791720.144588679039
1.9983-2.10360.17161380.137788979035
2.1036-2.23540.15461370.136689709107
2.2354-2.4080.17521370.144788939030
2.408-2.65030.16221620.136989429104
2.6503-3.03380.16231200.135889899109
3.0338-3.82190.17131560.127589729128
3.8219-44.70720.12951300.129791509280
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)
10.8245-0.1144-0.26311.20410.87471.2213-0.01480.1127-0.0839-0.035-0.08550.12880.1181-0.20240.0730.0839-0.017-0.01330.1061-0.00550.088-43.0152-7.096222.5264
20.56020.028-0.1380.51170.12810.6556-0.0113-0.0358-0.09650.03390.0114-0.10550.13040.1032-0.00320.09630.0177-0.00960.08120.01160.1037-20.9646-13.475733.1754
30.479-0.02870.08610.40350.28251.4625-0.0520.1038-0.1113-0.05520.0029-0.00680.1558-0.03070.04990.1613-0.0190.01090.1092-0.04330.1213-30.2443-20.11646.544
42.5275-0.70990.0532.58870.38442.564-0.0059-0.00360.1646-0.0715-0.04420.1494-0.0343-0.24470.01350.04930.0029-0.00390.0978-0.01970.0881-47.518915.6137.4579
50.96610.59990.15322.6580.94251.5306-0.02020.107-0.0608-0.20070.0203-0.0074-0.0048-0.0668-0.01230.08130.013-0.02790.08940.01610.0607-34.50223.976516.0007
61.39060.12150.66230.58320.12311.09760.0216-0.01880.0446-0.00350.004-0.1149-0.05640.1783-0.02060.0595-0.01630.00550.0932-0.0090.099-14.089511.184933.3609
71.8232-0.4518-0.52041.39710.61880.89580.0446-0.24430.25920.05910.0478-0.1452-0.13990.1947-0.07930.1151-0.0521-0.00060.1733-0.05040.1699-10.303923.291842.2814
80.66060.0463-0.12970.61450.21020.71170.0331-0.00040.0736-0.04130.0139-0.0924-0.05480.0769-0.03720.0697-0.01070.00310.07540.00530.079-21.631113.06326.7089
90.83610.0062-0.50980.90570.36792.49880.0746-0.05590.17880.05810.00250.0134-0.28460.0346-0.09630.1229-0.0050.01480.0857-0.02240.1356-37.212628.471744.5004
100.49960.0017-0.59660.7260.09791.207-0.0093-0.13020.01250.10860.0254-0.0071-0.06860.0508-0.00990.10550.0039-0.00240.1106-0.02480.0909-37.726718.001152.5932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 67 )A10 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 305 )A68 - 305
3X-RAY DIFFRACTION3chain 'A' and (resid 306 through 414 )A306 - 414
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 44 )B9 - 44
5X-RAY DIFFRACTION5chain 'B' and (resid 45 through 88 )B45 - 88
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 145 )B89 - 145
7X-RAY DIFFRACTION7chain 'B' and (resid 146 through 179 )B146 - 179
8X-RAY DIFFRACTION8chain 'B' and (resid 180 through 305 )B180 - 305
9X-RAY DIFFRACTION9chain 'B' and (resid 306 through 341 )B306 - 341
10X-RAY DIFFRACTION10chain 'B' and (resid 342 through 414 )B342 - 414

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