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- PDB-5t0z: PelC from Geobacter metallireducens -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5t0z
TitlePelC from Geobacter metallireducens
ComponentsLipoprotein, putative
KeywordsSTRUCTURAL PROTEIN / periplasmic / lipoprotein
Function / homologyLipoprotein, putative
Function and homology information
Biological speciesGeobacter metallireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.255 Å
AuthorsMarmont, L.S. / Howell, P.L.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Oligomeric lipoprotein PelC guides Pel polysaccharide export across the outer membrane of Pseudomonas aeruginosa.
Authors: Marmont, L.S. / Rich, J.D. / Whitney, J.C. / Whitfield, G.B. / Almblad, H. / Robinson, H. / Parsek, M.R. / Harrison, J.J. / Howell, P.L.
History
DepositionAug 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein, putative
B: Lipoprotein, putative
C: Lipoprotein, putative
D: Lipoprotein, putative


Theoretical massNumber of molelcules
Total (without water)78,9134
Polymers78,9134
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-26 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.931, 78.298, 85.136
Angle α, β, γ (deg.)90.00, 105.86, 90.00
Int Tables number4
Space group name H-MP1211
DetailsWhile PISA predicts a tetrameric assembly, the authors believe that is a crystallographic artifact. The related entry 5T11 displays the correct dodecameric assembly.

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Components

#1: Protein
Lipoprotein, putative


Mass: 19728.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (bacteria) / Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: Gmet_1966 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q39U79
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium cacodylate pH 6.5, 40% (v/v) MPD, 5% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 71358 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.696 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.255→46.423 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 3898 5.59 %
Rwork0.1729 --
obs0.1756 69701 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.255→46.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4550 0 0 169 4719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074628
X-RAY DIFFRACTIONf_angle_d0.8646304
X-RAY DIFFRACTIONf_dihedral_angle_d14.0952711
X-RAY DIFFRACTIONf_chiral_restr0.054742
X-RAY DIFFRACTIONf_plane_restr0.005813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2552-2.28270.28321070.26081985X-RAY DIFFRACTION82
2.2827-2.31160.29181350.25132379X-RAY DIFFRACTION100
2.3116-2.3420.27421330.2512351X-RAY DIFFRACTION100
2.342-2.37410.28181380.23782358X-RAY DIFFRACTION100
2.3741-2.4080.30111460.23872382X-RAY DIFFRACTION100
2.408-2.4440.30531460.23892335X-RAY DIFFRACTION100
2.444-2.48220.29371470.2162380X-RAY DIFFRACTION100
2.4822-2.52280.27521240.21532368X-RAY DIFFRACTION100
2.5228-2.56630.30161460.20782353X-RAY DIFFRACTION100
2.5663-2.6130.28491350.20732407X-RAY DIFFRACTION100
2.613-2.66330.27651270.20282332X-RAY DIFFRACTION100
2.6633-2.71760.26531460.19522403X-RAY DIFFRACTION100
2.7176-2.77670.2711650.19112278X-RAY DIFFRACTION100
2.7767-2.84130.24741190.18312455X-RAY DIFFRACTION100
2.8413-2.91230.20931410.17342339X-RAY DIFFRACTION100
2.9123-2.99110.27321480.17832403X-RAY DIFFRACTION100
2.9911-3.07910.25561540.18092289X-RAY DIFFRACTION100
3.0791-3.17840.19371330.17042390X-RAY DIFFRACTION100
3.1784-3.2920.24721270.16422388X-RAY DIFFRACTION100
3.292-3.42380.20831420.16042360X-RAY DIFFRACTION100
3.4238-3.57950.19551410.16062360X-RAY DIFFRACTION100
3.5795-3.76820.21171510.14612352X-RAY DIFFRACTION100
3.7682-4.00410.18261280.15262359X-RAY DIFFRACTION100
4.0041-4.31310.21891490.14582371X-RAY DIFFRACTION100
4.3131-4.74670.16531510.1422325X-RAY DIFFRACTION100
4.7467-5.43270.22641340.15992387X-RAY DIFFRACTION100
5.4327-6.84110.18751330.20072361X-RAY DIFFRACTION100
6.8411-46.43290.19821520.16762353X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.8631-2.74211.33823.4063-2.5162.71530.09360.30930.54610.32740.51480.2381-0.8074-0.8846-0.5660.57490.1237-0.02120.53930.06630.50598.615959.074357.5834
24.7795-1.20654.42045.5231-5.19777.37020.30980.7763-0.42960.1504-0.64970.21080.14730.48740.37570.4025-0.00120.03380.5186-0.01020.476925.106243.362866.0064
33.9132-0.2126-1.21238.9124-0.6987.1625-0.39060.0357-0.71430.22630.48440.17890.6163-0.0702-0.08910.4568-0.0416-0.00840.41030.0360.378817.696432.567972.5495
43.7742-3.367-3.46859.37284.02673.8180.32430.3329-0.835-0.47930.11440.82450.6371-0.6569-0.22450.6286-0.1135-0.17570.60640.06910.592110.581631.285566.944
56.24350.3664-3.2157.3453-2.34942.5924-0.08180.402-0.9734-1.26130.40980.38491.5122-0.48540.09260.8062-0.0673-0.06190.5273-0.1130.81817.100923.945167.6657
65.8422-3.6944-4.03832.27222.61063.64110.19941.0313-1.52520.8517-0.733.41730.3616-1.14110.46410.5899-0.0837-0.04270.79370.14921.21935.735132.323479.578
79.5086-5.887-1.67387.1681-0.03552.76660.6456-0.5709-1.0213-0.1104-0.28820.6510.36410.0091-0.3710.5952-0.0825-0.08290.50460.15180.535117.94527.24582.2016
86.2552-4.19972.6688.2339-3.85145.525-0.0037-0.1943-0.24790.35790.16540.4927-0.1632-0.2055-0.13950.3804-0.0346-0.01610.2539-0.0390.325514.472941.802368.7568
93.067-4.9285-1.35368.3884-0.28888.38210.01780.9916-0.4409-0.93690.08010.07470.39690.4389-0.12420.529-0.03860.00020.3594-0.01640.380118.212536.928761.9539
104.4119-0.62380.84861.9168-0.71972.1173-0.2807-0.8401-0.92640.02310.8080.43760.5505-0.9185-0.32950.7127-0.05840.06160.54560.0810.630417.824545.854678.2021
114.36-0.629-1.23376.8577-5.08884.58470.26180.48680.1871-0.14180.0928-0.28490.45140.3261-0.17070.44410.00710.07310.4877-0.01970.387921.606760.839361.7637
124.58871.2035-0.34558.4793-2.24513.80380.25310.31770.4221-0.2729-0.00810.0216-0.080.1964-0.26880.44930.08430.02770.341-0.04540.343311.847272.965161.5766
132.76854.24944.32538.58354.85479.3928-0.4165-0.10480.11960.18430.29420.2697-0.6325-0.06030.12990.51290.05940.03640.34070.01090.282411.70474.528770.4211
143.0834-0.1924-0.38942.5649-0.85582.4930.5330.06311.28480.5834-0.21290.4541-0.9471-0.0876-0.28880.70070.03570.13280.4096-0.01520.59669.15378.827265.055
154.7094.2928-6.00294.2084-5.30577.36420.02630.66010.1073-0.48080.08170.5061-0.9169-0.6846-0.21550.63270.1129-0.0710.47270.05140.60185.314879.02254.6847
162.67620.1457-0.16244.8986-4.05253.5738-0.1933-0.0619-0.221-0.19530.36470.7120.2087-0.0497-0.11460.580.08780.04570.3652-0.02930.41459.412263.722768.1925
173.21683.2297-3.19428.469-7.76947.7291-0.188-0.1919-0.2166-0.6530.22310.05620.6996-0.10030.30630.52860.06560.09130.3269-0.02620.367812.919861.946467.5573
181.819-0.2931.46674.6504-5.66118.46340.0170.35310.0434-0.32170.11420.3547-0.6918-0.0728-0.23610.79480.10940.0060.4077-0.04750.364415.814669.201956.3627
195.53910.311-2.82236.12865.99957.9971-0.3786-2.6729-0.16122.10041.2539-0.8787-1.30021.128-0.7020.7608-0.07560.00320.7054-0.02190.376516.403957.591281.7383
203.18514.08-1.91958.4037-5.46953.5393-0.275-0.49670.35030.5845-0.3847-0.659-0.75250.69940.49740.5180.0367-0.06360.42570.02280.553220.827669.350667.491
210.836-2.06740.89574.8492-2.15550.9536-0.4252.14481.82190.47950.293-0.9235-1.58940.95310.52890.9496-0.30390.06050.93170.2990.558726.916862.800951.1666
223.17761.6708-2.21065.6149-5.71035.8823-0.1838-0.3785-1.03140.003-0.9028-0.5593-0.3-0.50740.81760.4173-0.0486-0.00050.44450.04530.506424.431752.595172.6215
236.95581.39413.75132.13068.15568.36962.1686-2.9649-1.63062.51980.33450.22583.35610.3403-1.24161.3675-0.2555-0.10921.15120.05460.735628.484350.851489.899
246.4414-0.02632.79475.5133-0.09584.13470.3324-0.1547-0.01450.50180.0467-1.06440.46490.2163-0.39160.3663-0.0245-0.10260.4777-0.08370.640242.007255.787475.8063
257.3442-4.57883.4879.538-6.12459.7132-0.3276-1.65390.66640.97760.6352-0.6523-0.87470.4922-0.20780.5611-0.0796-0.01090.7511-0.17840.516939.027858.616887.5818
261.82180.74541.0343.31783.92415.17930.7412-0.8229-0.74641.45740.5637-1.43880.9593-0.6443-0.75920.72020.1231-0.49380.91780.1021.252644.940345.7483.7173
274.8909-0.2088-0.33386.1306-3.63726.05460.23770.1371-0.1999-0.45150.5029-0.65040.95890.5625-0.36910.2823-0.0759-0.00410.4963-0.02050.59938.05654.576968.1972
286.61531.5275-2.13445.4945-2.04986.31030.0818-0.4366-0.78260.3324-0.2823-0.67450.11820.2280.17590.3893-0.0339-0.14910.3239-0.02790.549232.759851.544473.3833
296.90771.84523.91518.3725-2.34377.2349-0.1124-0.03311.00360.45620.0435-0.4669-0.96731.3665-0.14830.6959-0.20710.17090.641-0.02090.70333.483567.936759.9273
304.81773.2609-4.73743.6553-3.75444.2435-0.0059-0.23521.06980.88470.5802-0.01930.05620.0746-0.52050.55260.0226-0.11060.4617-0.03390.528730.649260.114775.7712
316.7610.7292.41119.0241-0.27612.1164-0.46080.2532-0.18790.088-0.0643-0.77460.13611.26590.48530.40670.0377-0.04160.570.00930.608334.067743.731867.6533
325.1811-5.4382.54216.1115-3.46412.9081-0.1894-0.21620.69270.45510.1007-0.5026-1.4038-0.36310.08070.53390.039-0.00970.39140.01780.391117.254653.449556.4472
333.9696-1.5486-3.8815.88780.88293.9485-0.48591.74130.3763-0.4237-0.54610.7807-2.3414-2.4680.89371.09140.1147-0.19141.0797-0.17380.65876.858253.870841.0912
343.70222.8048-1.61383.38070.20475.052-0.58360.6368-0.0411-0.95860.468-0.326-1.96770.689-0.1220.9738-0.18310.18710.7689-0.12030.421328.233654.547741.729
356.77280.2386-0.18885.0886-1.07869.52320.01010.25750.2731-0.9183-0.0616-0.1559-0.54720.16170.07770.7075-0.02970.07750.4887-0.12490.381622.874548.301638.067
367.11831.31981.752.25012.74584.171-0.14961.46351.5544-1.7429-0.41970.2438-3.6353-0.3830.08812.11150.10190.21150.97290.26790.528519.527560.988332.3865
373.95020.05120.10735.0944-0.84885.741-0.05480.59520.2712-0.40740.0294-0.734-1.53220.9919-0.04580.6774-0.08240.13640.5808-0.10010.36829.445751.723848.6821
383.75160.1210.23964.1948-0.81944.55490.48990.20070.0397-0.9877-0.0506-0.3338-0.37180.2622-0.20760.6814-0.01890.14980.371-0.09550.330926.742651.242851.3415
393.45561.2930.87062.5642-3.39959.0380.5740.68120.5594-1.3877-0.15640.435-1.1043-0.6091-0.09581.14250.2482-0.04540.5556-0.00830.382616.170657.977146.3319
405.3821-0.2614-4.1423.2815-0.60733.44090.62331.0336-0.0117-0.86810.1537-1.04650.40410.576-0.61720.65890.03040.19750.5978-0.12310.652832.930238.53157.4526
412.2925-1.69553.11644.3407-0.92125.9877-0.4218-0.2431-0.4658-0.57480.45070.2177-0.1246-0.2115-0.10060.606-0.0584-0.00320.4455-0.05860.324819.092445.876949.0651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 25 )
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 50 )
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 65 )
5X-RAY DIFFRACTION5chain 'A' and (resid 66 through 73 )
6X-RAY DIFFRACTION6chain 'A' and (resid 74 through 90 )
7X-RAY DIFFRACTION7chain 'A' and (resid 91 through 107 )
8X-RAY DIFFRACTION8chain 'A' and (resid 108 through 158 )
9X-RAY DIFFRACTION9chain 'A' and (resid 159 through 179 )
10X-RAY DIFFRACTION10chain 'B' and (resid 12 through 17 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 25 )
12X-RAY DIFFRACTION12chain 'B' and (resid 26 through 50 )
13X-RAY DIFFRACTION13chain 'B' and (resid 51 through 65 )
14X-RAY DIFFRACTION14chain 'B' and (resid 66 through 90 )
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 107 )
16X-RAY DIFFRACTION16chain 'B' and (resid 108 through 121 )
17X-RAY DIFFRACTION17chain 'B' and (resid 122 through 137 )
18X-RAY DIFFRACTION18chain 'B' and (resid 138 through 152 )
19X-RAY DIFFRACTION19chain 'B' and (resid 153 through 158 )
20X-RAY DIFFRACTION20chain 'B' and (resid 159 through 180 )
21X-RAY DIFFRACTION21chain 'C' and (resid 12 through 17 )
22X-RAY DIFFRACTION22chain 'C' and (resid 18 through 25 )
23X-RAY DIFFRACTION23chain 'C' and (resid 26 through 36 )
24X-RAY DIFFRACTION24chain 'C' and (resid 37 through 65 )
25X-RAY DIFFRACTION25chain 'C' and (resid 66 through 73 )
26X-RAY DIFFRACTION26chain 'C' and (resid 74 through 107 )
27X-RAY DIFFRACTION27chain 'C' and (resid 108 through 121 )
28X-RAY DIFFRACTION28chain 'C' and (resid 122 through 152 )
29X-RAY DIFFRACTION29chain 'C' and (resid 153 through 158 )
30X-RAY DIFFRACTION30chain 'C' and (resid 159 through 178 )
31X-RAY DIFFRACTION31chain 'D' and (resid 12 through 18 )
32X-RAY DIFFRACTION32chain 'D' and (resid 19 through 25 )
33X-RAY DIFFRACTION33chain 'D' and (resid 26 through 36 )
34X-RAY DIFFRACTION34chain 'D' and (resid 37 through 50 )
35X-RAY DIFFRACTION35chain 'D' and (resid 51 through 90 )
36X-RAY DIFFRACTION36chain 'D' and (resid 91 through 107 )
37X-RAY DIFFRACTION37chain 'D' and (resid 108 through 121 )
38X-RAY DIFFRACTION38chain 'D' and (resid 122 through 137 )
39X-RAY DIFFRACTION39chain 'D' and (resid 138 through 152 )
40X-RAY DIFFRACTION40chain 'D' and (resid 153 through 158 )
41X-RAY DIFFRACTION41chain 'D' and (resid 159 through 178 )

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