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- PDB-6hrc: Outward-facing PglK with ATPgammaS bound -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6hrc
TitleOutward-facing PglK with ATPgammaS bound
ComponentsWlaB protein
KeywordsTRANSPORT PROTEIN / ABC transporter
Function / homology
Function and homology information


ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / WlaB protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsPerez, C. / Locher, K.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_166672 Switzerland
CitationJournal: Structure / Year: 2019
Title: Structure of Outward-Facing PglK and Molecular Dynamics of Lipid-Linked Oligosaccharide Recognition and Translocation.
Authors: Perez, C. / Mehdipour, A.R. / Hummer, G. / Locher, K.P.
History
DepositionSep 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WlaB protein
B: WlaB protein
C: WlaB protein
D: WlaB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,38010
Polymers258,2384
Non-polymers2,1426
Water2,450136
1
A: WlaB protein
B: WlaB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1905
Polymers129,1192
Non-polymers1,0713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14820 Å2
ΔGint-109 kcal/mol
Surface area49900 Å2
MethodPISA
2
C: WlaB protein
D: WlaB protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,1905
Polymers129,1192
Non-polymers1,0713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14840 Å2
ΔGint-104 kcal/mol
Surface area50130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.680, 145.980, 206.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
WlaB protein /


Mass: 64559.621 Da / Num. of mol.: 4 / Mutation: E510Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: wlaB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O86150
#2: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: Na3Citrate: NaCl:MgCl2:ATPgammaS:PEG400

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→19.995 Å / Num. obs: 52311 / % possible obs: 90.83 % / Redundancy: 13.8 % / Rrim(I) all: 0.181 / Net I/σ(I): 1.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.3813.1511.9771.611100.4592.05724.7
3.38-3.4813.4112.1971.4421650.4362.28349.5
3.48-3.5812.3782.2851.3140480.4042.38495.2
3.58-3.713.7371.7131.9241210.6011.77899.9
3.7-3.8314.2261.1982.9140130.81.242100
3.83-3.9714.0860.9843.5238430.8541.021100
3.97-4.1413.930.7214.6837140.9010.748100
4.14-4.3213.7360.5056.3335800.9420.524100
4.32-4.5313.3050.3558.6434090.9680.369100
4.53-4.7812.1940.24811.1332610.980.25999.7
4.78-5.0714.1610.23213.0631100.9880.241100
5.07-5.4214.0730.21913.3929120.9880.227100
5.42-5.8513.8350.23412.5127270.9870.243100
5.85-6.4113.3110.19214.5625100.990.2100
6.41-7.1611.9210.13118.7422720.9940.13799.7
7.16-8.2713.7170.07332.0620470.9990.076100
8.27-10.1313.0810.04346.9417360.9990.045100
10.13-14.3311.4710.03750.6613570.9990.03999.2
14.33-24.95212.2940.03257.817080.9990.03387.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C78

5c78


Resolution: 3.3→19.995 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.53
RfactorNum. reflection% reflection
Rfree0.2838 2665 5.09 %
Rwork0.2323 --
obs0.2349 52311 90.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 602.5 Å2 / Biso mean: 143.8265 Å2 / Biso min: 34.3 Å2
Refinement stepCycle: final / Resolution: 3.3→19.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18220 0 126 136 18482
Biso mean--111.82 39.29 -
Num. residues----2256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3002-3.35990.467360.397367070624
3.3599-3.42420.4009630.36821103116639
3.4242-3.49380.4148950.361811190663
3.4938-3.56930.37711370.35842815295299
3.5693-3.65190.39971640.344228192983100
3.6519-3.74260.40341580.307928332991100
3.7426-3.84310.36341410.291828783019100
3.8431-3.95540.3161440.287228522996100
3.9554-4.0820.32971700.276528423012100
4.082-4.22660.3141560.256328483004100
4.2266-4.39410.25391510.22728773028100
4.3941-4.59180.27271440.211328773021100
4.5918-4.83060.2551500.192228653015100
4.8306-5.12850.25681600.198128593019100
5.1285-5.51670.26361480.20629143062100
5.5167-6.05790.28681570.227429053062100
6.0579-6.90270.31381610.23829133074100
6.9027-8.58070.28751650.211229373102100
8.5807-19.99580.20281650.180430283193100
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)
15.68742.0667-1.74212.937-1.92522.81570.6412-0.86371.61670.5689-0.8802-0.344-1.97390.95910.00772.2461-0.70380.25811.62-0.48861.825625.99817.228819.4419
22.10662.5068-1.64972.5871-2.28913.90990.7966-0.92520.35020.7476-0.7442-0.4199-1.39181.5956-0.08791.1787-0.36680.17371.5805-0.45361.107819.33840.631121.1655
33.70270.08510.78683.4455-0.84053.48980.4087-1.24691.18090.9922-0.5071-0.1752-1.10950.95060.0690.9854-0.19840.2011.0901-0.43930.8752.2011-0.839628.2419
41.82171.4738-0.02195.26090.36210.0241-0.2986-0.48021.33290.68110.4199-0.1323-0.16420.2382-0.06681.05270.1117-0.12730.8585-0.40881.5188-8.55422.280919.9283
57.48984.5631-1.7059.3286-3.63764.0663-0.69791.19981.8064-1.12690.88610.7243-1.34971.5243-0.16031.6643-0.4991-0.05361.30090.0290.7836-6.00410.83410.5162
65.7216-1.79042.82220.73670.06354.043-0.86981.39854.4815-0.61810.5716-1.0226-1.75362.35930.40932.3273-2.17210.5072-0.5601-1.92083.78239.264824.117112.8448
74.27630.07931.83712.6977-1.34461.8011-0.7796-2.19610.30770.28050.81820.10350.5264-1.02290.0361.35680.08120.32042.182-0.05840.6683-11.0857-25.053448.8673
82.5347-0.1621-1.27784.3871.15928.0566-0.4267-1.3567-0.32120.73090.46570.10.69090.628-0.09430.65930.0956-0.04311.38430.2760.6709-5.4313-39.151137.5816
91.9321-0.35392.70387.9006-0.39144.3178-0.0094-2.3376-2.02670.60230.03942.3081.49850.1913-0.01431.67440.14280.49951.82260.88791.1648-16.8397-46.286448.1152
102.9547-0.14491.29196.2501-2.92691.81980.28950.69970.767-0.41810.11920.66210.45520.2486-0.45251.8082-0.03160.4030.9946-0.05770.6272-3.35320.0631-4.7771
116.08361.29512.59524.1594-5.23869.7032-0.0623.53781.0462-0.0170.1385-0.7912-3.03352.26340.23312.7887-0.81780.75652.36730.28812.627810.416835.0364-12.18
121.05140.2715-0.80094.4819-2.72043.79760.4190.141.0911-0.152-0.4768-0.6785-0.49780.88130.11110.7333-0.15620.26090.6580.0181.0865-6.1367-2.22716.0968
134.83773.1267-4.63086.6071-5.3867.0344-0.0917-0.1530.4978-0.57130.0608-0.7675-0.15120.37680.04320.7484-0.1730.12450.9473-0.28870.812910.0019-8.49188.7027
146.34940.0386-2.40714.1139-0.41537.76950.1693-0.68091.3425-0.7118-0.0029-1.2337-0.69990.76280.28960.7369-0.0742-0.03821.0326-0.27631.24218.0466-3.205613.6425
156.17772.64164.57356.34260.6683.7467-0.7759-0.25161.92260.0755-0.26911.7205-2.58272.16020.82321.7508-0.53030.331.4226-0.18871.848920.489410.9126-1.9365
167.23692.9305-2.02182.6976-2.77793.00430.23810.3468-0.98980.2435-0.3586-0.41510.54940.03740.18120.77670.04210.05570.4583-0.14480.9726-22.1358-38.83138.6645
173.84232.55422.49256.95811.53224.06660.219-1.5958-0.15450.87640.03120.4975-0.0984-0.7865-0.11650.6820.03270.3161.32190.22820.781-30.5744-28.424430.3916
186.8683-2.19572.33088.8857-0.4542.93690.9375-2.1053-2.18211.2448-0.7041.58760.8718-1.4004-0.30981.0265-0.25720.34961.41490.28381.6926-32.3465-48.300324.0288
191.398-2.1432-1.09375.39233.94923.07350.4933-1.04230.65790.68810.1080.0553-3.19260.3152-0.29431.5802-0.3114-0.32211.2337-0.16780.959727.6307-31.921636.4718
200.8734-0.8046-0.04163.49790.34640.9146-0.67090.65611.129-0.14470.0444-0.8721-0.46431.0553-0.01344.3337-0.2698-2.17383.2552-1.18942.253441.0671-25.586672.2686
212.97141.0882.12451.56611.62517.9068-0.9319-2.08371.76210.5793-1.59410.8748-0.09580.15541.9131.071-0.0928-0.11331.8711-0.14840.858325.1141-39.766744.4576
221.33390.14990.73683.81120.45473.8606-1.0263-0.91821.2510.49640.3306-0.4176-1.36131.14070.37370.9641-0.053-0.48361.3616-0.37271.246130.5825-41.238826.5968
236.3823.45351.39366.74094.59074.5801-0.4374-0.93271.64670.21910.2850.7293-0.37870.98450.08770.7513-0.1029-0.26530.8591-0.11141.141841.6281-49.466924.3668
249.23995.1253.80797.11213.90997.35840.1732-1.3544-0.161.04840.1694-0.84670.19181.8126-0.72451.0020.0163-0.30441.38040.0021.118450.0805-50.094934.1276
251.99470.1826-1.16130.2604-0.55941.5277-0.2631-1.48490.96471.28760.3812-0.76420.11881.3234-0.0571.43270.3211-0.73881.8035-0.41.688650.9626-34.947747.5466
266.58121.32943.64514.12793.53775.00810.14960.78920.5044-0.35260.42580.28520.12390.4108-0.58610.6799-0.1161-0.1140.89440.23810.799811.6519-45.7421-1.8007
275.75090.1756-0.00387.4212-1.72595.42970.14910.508-0.68950.08040.23291.00930.4794-0.5551-0.30110.545-0.2343-0.0560.68540.0590.83422.0021-60.35145.5545
287.5974.6727-5.54558.514-3.33028.71540.62932.06-2.35540.0346-0.49610.2704-0.003-1.7003-0.21220.5986-0.1029-0.25871.429-0.10741.1106-1.0513-61.1001-11.2947
292.9268-0.84310.55612.5843-2.12290.97470.9772-2.118-0.78342.2008-0.1254-2.121.0206-0.0354-0.74021.70290.2763-0.75492.0006-0.07671.559355.2396-56.413448.8061
303.3772-0.86391.51111.1974-0.3654.8592-0.1407-1.9723-0.61520.62980.5918-0.21190.468-0.2387-0.45771.00880.1099-0.13361.63780.34740.797727.3524-61.004636.9433
313.1415-1.41160.75251.9323-1.71868.0278-0.2985-1.58340.28380.7713-0.2189-0.6457-0.90182.46470.26821.4625-0.1374-0.41972.33130.15690.927132.6857-48.814254.2835
321.7238-1.01390.19020.38410.25413.6704-0.331-0.3454-1.23170.01960.18560.83271.06940.0960.24221.4305-0.0743-0.00980.5940.17831.811121.7876-86.78199.8818
336.5785-0.2445-0.20384.85852.93698.09530.2536-0.0219-0.3521-0.7124-0.19820.23150.136-0.1305-0.07680.701-0.1229-0.19880.4814-0.07980.941526.4117-67.885-6.5984
349.26763.7679-0.8727.3058-1.96416.00590.6160.3303-2.384-0.7533-0.18421.07921.6712-0.8382-0.39741.3216-0.3384-0.30280.9452-0.08061.708414.5494-84.8783-9.5077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 70 )A1 - 70
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 117 )A71 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 169 )A118 - 169
4X-RAY DIFFRACTION4chain 'A' and (resid 170 through 231 )A170 - 231
5X-RAY DIFFRACTION5chain 'A' and (resid 232 through 279 )A232 - 279
6X-RAY DIFFRACTION6chain 'A' and (resid 280 through 319 )A280 - 319
7X-RAY DIFFRACTION7chain 'A' and (resid 320 through 388 )A320 - 388
8X-RAY DIFFRACTION8chain 'A' and (resid 389 through 519 )A389 - 519
9X-RAY DIFFRACTION9chain 'A' and (resid 520 through 564 )A520 - 564
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 35 )B1 - 35
11X-RAY DIFFRACTION11chain 'B' and (resid 36 through 68 )B36 - 68
12X-RAY DIFFRACTION12chain 'B' and (resid 69 through 151 )B69 - 151
13X-RAY DIFFRACTION13chain 'B' and (resid 152 through 232 )B152 - 232
14X-RAY DIFFRACTION14chain 'B' and (resid 233 through 277 )B233 - 277
15X-RAY DIFFRACTION15chain 'B' and (resid 278 through 319 )B278 - 319
16X-RAY DIFFRACTION16chain 'B' and (resid 320 through 423 )B320 - 423
17X-RAY DIFFRACTION17chain 'B' and (resid 424 through 522 )B424 - 522
18X-RAY DIFFRACTION18chain 'B' and (resid 523 through 564 )B523 - 564
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 34 )C1 - 34
20X-RAY DIFFRACTION20chain 'C' and (resid 35 through 70 )C35 - 70
21X-RAY DIFFRACTION21chain 'C' and (resid 71 through 117 )C71 - 117
22X-RAY DIFFRACTION22chain 'C' and (resid 118 through 169 )C118 - 169
23X-RAY DIFFRACTION23chain 'C' and (resid 170 through 231 )C170 - 231
24X-RAY DIFFRACTION24chain 'C' and (resid 232 through 279 )C232 - 279
25X-RAY DIFFRACTION25chain 'C' and (resid 280 through 319 )C280 - 319
26X-RAY DIFFRACTION26chain 'C' and (resid 320 through 388 )C320 - 388
27X-RAY DIFFRACTION27chain 'C' and (resid 389 through 519 )C389 - 519
28X-RAY DIFFRACTION28chain 'C' and (resid 520 through 564 )C520 - 564
29X-RAY DIFFRACTION29chain 'D' and (resid 1 through 113 )D1 - 113
30X-RAY DIFFRACTION30chain 'D' and (resid 114 through 232 )D114 - 232
31X-RAY DIFFRACTION31chain 'D' and (resid 233 through 319 )D233 - 319
32X-RAY DIFFRACTION32chain 'D' and (resid 320 through 423 )D320 - 423
33X-RAY DIFFRACTION33chain 'D' and (resid 424 through 522 )D424 - 522
34X-RAY DIFFRACTION34chain 'D' and (resid 523 through 564 )D523 - 564

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Jul 12, 2017. Major update of PDB

Major update of PDB

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

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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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