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- PDB-5d0q: BamACDE complex, outer membrane beta-barrel assembly machinery (B... -

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Basic information

Entry
Database: PDB / ID: 5d0q
TitleBamACDE complex, outer membrane beta-barrel assembly machinery (BAM) complex
Components
  • Outer membrane protein assembly factor BamA
  • Outer membrane protein assembly factor BamC
  • Outer membrane protein assembly factor BamD
  • Outer membrane protein assembly factor BamE
KeywordsPROTEIN TRANSPORT / outer membrane biogenesis / outer membrane beta-barrel assembly machinery complex / E.coli / outer membrane insertion.
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / protein-macromolecule adaptor activity / cell adhesion / response to antibiotic / cell surface / membrane / identical protein binding
Similarity search - Function
Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like ...Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / SmpA / OmlA family / Outer membrane lipoprotein / BamE-like / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamD
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsGu, Y. / Paterson, N. / Zeng, Y. / Dong, H. / Wang, W. / Dong, C.
CitationJournal: Nature / Year: 2016
Title: Structural basis of outer membrane protein insertion by the BAM complex.
Authors: Gu, Y. / Li, H. / Dong, H. / Zeng, Y. / Zhang, Z. / Paterson, N.G. / Stansfeld, P.J. / Wang, Z. / Zhang, Y. / Wang, W. / Dong, C.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
C: Outer membrane protein assembly factor BamC
D: Outer membrane protein assembly factor BamD
E: Outer membrane protein assembly factor BamE
F: Outer membrane protein assembly factor BamA
G: Outer membrane protein assembly factor BamC
I: Outer membrane protein assembly factor BamE
H: Outer membrane protein assembly factor BamD


Theoretical massNumber of molelcules
Total (without water)341,3798
Polymers341,3798
Non-polymers00
Water0
1
A: Outer membrane protein assembly factor BamA
C: Outer membrane protein assembly factor BamC
D: Outer membrane protein assembly factor BamD
E: Outer membrane protein assembly factor BamE


Theoretical massNumber of molelcules
Total (without water)170,6894
Polymers170,6894
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-57 kcal/mol
Surface area67330 Å2
MethodPISA
2
F: Outer membrane protein assembly factor BamA
G: Outer membrane protein assembly factor BamC
I: Outer membrane protein assembly factor BamE
H: Outer membrane protein assembly factor BamD


Theoretical massNumber of molelcules
Total (without water)170,6894
Polymers170,6894
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-50 kcal/mol
Surface area57840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)254.157, 254.157, 179.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Outer membrane protein assembly factor BamA / Omp85


Mass: 91393.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A940
#2: Protein Outer membrane protein assembly factor BamC


Mass: 37297.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamC, dapX, nlpB, b2477, JW2462 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A903
#3: Protein Outer membrane protein assembly factor BamD


Mass: 28280.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamD, yfiO, b2595, JW2577 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC02
#4: Protein Outer membrane protein assembly factor BamE


Mass: 13717.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamE, smpA, b2617, JW2598 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A937

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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: 4.28 Å3/Da / Density % sol: 71.29 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris, pH8.0, 0.1 M MgCl2, 24% PEG500 MME. / PH range: 7.8-8.2

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Data collection

DiffractionMean temperature: 197 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→29.94 Å / Num. obs: 74050 / % possible obs: 99.8 % / Redundancy: 26.9 % / Net I/av σ(I): 1.5 / Net I/σ(I): 8.2
Reflection shellResolution: 3.5→3.58 Å / Redundancy: 24.7 % / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
SCALAdata scaling
SHELXDEphasing
RefinementResolution: 3.5→29.943 Å / SU ML: 1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 44.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3399 3727 5.03 %
Rwork0.3142 --
obs0.3154 74044 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→29.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19900 0 0 0 19900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00620334
X-RAY DIFFRACTIONf_angle_d1.18627609
X-RAY DIFFRACTIONf_dihedral_angle_d17.6927430
X-RAY DIFFRACTIONf_chiral_restr0.0462982
X-RAY DIFFRACTIONf_plane_restr0.0053660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.54420.47781420.47342553X-RAY DIFFRACTION100
3.5442-3.59080.48281410.47322585X-RAY DIFFRACTION100
3.5908-3.63990.48271190.45032557X-RAY DIFFRACTION100
3.6399-3.69180.47061400.46312596X-RAY DIFFRACTION100
3.6918-3.74680.45151330.44672570X-RAY DIFFRACTION100
3.7468-3.80530.4141340.42412537X-RAY DIFFRACTION100
3.8053-3.86750.43121360.4092589X-RAY DIFFRACTION100
3.8675-3.93410.4211220.4112595X-RAY DIFFRACTION100
3.9341-4.00540.42031510.4072547X-RAY DIFFRACTION100
4.0054-4.08230.42471200.39622614X-RAY DIFFRACTION100
4.0823-4.16540.39341360.39082584X-RAY DIFFRACTION100
4.1654-4.25570.36481530.38472556X-RAY DIFFRACTION100
4.2557-4.35440.40991330.36632579X-RAY DIFFRACTION100
4.3544-4.4630.34911500.34682585X-RAY DIFFRACTION100
4.463-4.58320.35461390.32912596X-RAY DIFFRACTION100
4.5832-4.71760.36231270.33342603X-RAY DIFFRACTION100
4.7176-4.86930.32551570.33162569X-RAY DIFFRACTION100
4.8693-5.04250.36781310.32742587X-RAY DIFFRACTION100
5.0425-5.24340.35791230.33822611X-RAY DIFFRACTION100
5.2434-5.48060.35681410.3482613X-RAY DIFFRACTION100
5.4806-5.76760.35131430.34542626X-RAY DIFFRACTION100
5.7676-6.12610.37591510.3452595X-RAY DIFFRACTION100
6.1261-6.59450.34761260.31722643X-RAY DIFFRACTION100
6.5945-7.24960.31331580.29682638X-RAY DIFFRACTION100
7.2496-8.27910.31471400.26712657X-RAY DIFFRACTION100
8.2791-10.35860.22561510.20252695X-RAY DIFFRACTION100
10.3586-29.94450.2861300.24132837X-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)
11.3792-0.45550.18512.783-1.73060.79310.79840.349-0.0639-0.8249-0.7638-0.05470.0858-0.6450.00021.5999-0.1519-0.20671.32190.16141.589-66.8782-87.2458-2.4922
2-0.46190.4392-0.52270.99040.69822.39490.07180.1484-0.65890.43940.44950.31610.5182-0.5415-0.00031.57270.0132-0.33531.35480.12171.9349-81.6276-86.5644-47.2978
30.5227-0.4542-0.00450.859-0.61232.6570.0047-0.1343-0.5896-0.43620.0280.102-0.19590.668601.2203-0.28110.08391.2096-0.03651.181-43.8111-66.0007-49.8587
40.7469-0.6112-0.82591.06850.13020.7859-0.27121.1479-0.3814-0.22560.1257-0.24850.45790.0363-0.00011.3679-0.18690.0151.7847-0.40181.3478-33.0192-83.4004-66.6172
51.8371.6776-0.6281.56630.35642.7318-0.1109-0.12731.4883-0.9982-0.0306-3.1145-0.0137-0.3607-0.00171.1323-0.19370.21341.07120.19721.4182-38.6806-51.0398-18.3429
61.1132-1.9952-1.06080.86370.4080.6975-0.28020.31560.17420.86010.4687-0.3434-0.3397-0.78290.00060.9742-0.0655-0.25020.8994-0.13321.2543-46.6927-60.8468-4.8974
70.9127-0.24780.13860.72820.57070.57561.03850.6645-0.3820.08380.81720.4047-1.28220.21040.00021.6089-0.10490.0251.41840.17141.3275-43.4101-79.034919.1184
81.3204-0.40710.91982.54980.85232.6354-0.46360.031-0.8372-0.11350.1781-0.47460.48170.1184-0.00041.11060.08440.05341.52390.11831.1974-36.5477-73.348813.0511
90.17770.0989-0.39092.32560.35150.6619-0.0968-0.5512-1.4577-0.7487-0.24021.42770.34930.2987-0.00031.6508-0.0362-0.26491.37930.14742.2058-50.2771-111.47020.638
101.73390.5071-0.29071.19710.81291.09260.32510.0275-0.323-0.2576-0.36180.32750.240.098201.0564-0.29460.07221.19740.06671.2279-44.4005-75.9453-9.7682
110.04290.041-0.10440.27630.16950.1164-0.15590.1542-0.27841.34430.1469-0.6726-1.59730.7871-0.0011.64590.1534-0.18891.01090.16881.0446-39.5314-60.2243-32.6888
123.0695-0.63790.13093.15541.6120.6332-00.14030.5412-0.5277-0.1822-0.6533-0.1861-0.514-0.00021.12410.16380.13890.66480.10941.01-48.5401-53.0931-22.6612
130.3599-0.4048-0.08541.11140.45950.17790.6863-0.33051.0457-0.1847-0.4262-0.042-0.6262-0.23010.00011.5654-0.0250.10621.28910.13951.1604-53.4347-37.4794-36.6414
141.27320.8177-1.00742.0085-0.72270.8539-1.5704-1.57560.5869-0.35980.64-0.7273-1.2393-1.5405-0.06911.39560.3029-0.40491.78320.08740.6081-53.5939-49.8539-60.2376
150.0474-0.0237-0.0634-0.00070.05310.0808-0.20190.5394-0.0402-1.2902-0.124-1.4339-0.8927-0.8191-0.00231.27470.2115-0.05711.9105-0.54621.315-70.2752-44.7064-49.4283
160.31940.31250.01860.18250.02190.08910.0942-0.2790.3327-0.80721.2412.2961-1.5558-1.3785-0.00482.15090.0969-0.49171.65410.27071.9621-81.2381-37.4171-41.9725
170.62420.23260.77580.30070.10450.88580.66011.5815-2.9239-1.2898-0.3274-0.51860.82881.03970.05011.347-0.35210.09960.33880.9271.5798-67.4178-37.1013-36.0526
18-0.1665-0.1485-0.21350.0875-0.20950.09090.03561.4161-1.0518-0.065-0.96240.95570.962-0.5613-0.00331.3198-0-0.28550.9989-0.24271.2042-64.1858-41.3857-51.2022
19-0.03930.1028-0.4013-0.01530.28231.46191.9883-0.07780.03720.0942-1.75891.31-0.1208-1.71160.03342.03650.2414-0.64721.03050.06041.4002-72.1205-30.5737-42.5281
201.71781.47981.32021.56440.06060.8849-0.28780.0619-0.3199-0.23990.3563-0.8048-0.3309-0.13890.00022.0468-0.13180.30571.5701-0.23651.612-54.0886-93.6916-147.0028
211.68611.3322-0.50071.7476-1.10611.2332-0.1079-0.4273-0.68990.5138-0.1905-0.34860.41211.46440.00011.4611-0.0363-0.05451.7539-0.02881.4328-24.9502-77.0556-117.4648
22-0.04510.25550.37071.3297-0.74220.86550.1314-0.096-0.06930.103-0.0311-0.51620.31750.1114-01.45410.10030.08851.44970.05281.4917-35.8625-120.8829-96.1695
232.99140.0321.25850.10030.15960.9598-0.95531.6377-0.97620.59760.2132-0.6651-0.90431.244-0.07431.937-1.1424-0.10221.32610.37261.6544-66.3949-129.0642-130.6191
240.96140.72690.97110.28120.6870.7101-0.4659-0.4095-0.306-0.58850.12430.5861-0.12-2.1679-0.00311.6156-0.29020.17390.59880.08121.2564-82.2827-106.292-112.0583
250.7041-0.38150.24040.60870.50.7092-0.5039-0.4432-1.34611.13340.30730.7796-0.149-0.20310.21361.6169-0.0516-0.41090.6904-0.08691.6146-76.3199-115.6654-128.924
260.16620.0385-0.10430.1156-0.06970.4581-0.2383-0.61690.66670.5292-0.12710.0082-0.3125-2.5006-0.00331.8177-0.3187-0.0962.15450.10910.9941-71.0169-119.7139-145.9877
270.10650.06-0.07750.0974-0.03170.0641-0.2094-0.2803-0.5182-0.44221.36311.4858-0.4984-0.132-0.00872.10930.10320.27174.10240.22262.1865-72.1576-123.7762-150.4674
280.07050.01260.0096-0.00640.0118-0.0003-0.5804-0.30650.212-1.2170.45920.28510.34660.56580.00482.1072-1.7073-0.00842.8252-0.16323.4052-62.1628-124.9946-164.3866
293.39842.49920.01763.49630.81360.3647-0.24880.4893-1.8223-0.2532-0.1768-0.2044-1.5433-0.51860.18820.57980.75040.60861.2186-0.10291.6736-55.6192-105.6206-84.3111
301.4814-0.4080.80660.49530.26280.9038-1.9012-0.5767-0.27680.574-0.6105-1.0796-0.68290.0517-0.9669-1.44673.25780.0352-1.0738-1.11172.296-62.069-87.8369-92.2952
310.2256-0.0330.04220.38930.14860.0456-0.7034-1.20140.239-0.7904-0.34881.01970.1443-1.1323-0.00022.0418-0.151-0.15821.0004-0.31531.8533-69.2629-75.3513-96.3869
325.30980.17571.51850.04680.4813.4039-1.2841-1.83630.12571.3173-0.88180.30240.2937-0.5062-1.34761.16152.32211.2950.6219-0.0611.4189-74.5658-88.6257-101.1492
330.16320.2246-0.140.0585-0.41960.0031.8067-1.84662.0047-0.4461-2.0920.06320.3010.3492-0.00220.0921-1.13071.02822.28890.40160.957-65.0012-93.2014-89.1985
343.84542.8358-1.55893.003-1.38780.8752-0.47162.96433.77450.11940.80733.42060.1169-1.10210.17241.21360.27670.3061-0.6203-1.4070.9629-76.7007-82.9012-92.677
350.5526-0.4365-0.99241.6408-0.34691.69770.10470.88040.2709-1.0992-0.3755-0.34061.2444-0.065-0.00072.93460.16510.45311.13280.2171.2541-57.4763-117.1104-141.1137
360.04720.0344-0.14220.3317-0.20180.5396-0.31970.8303-0.8561-1.4293-0.6812-0.28151.4557-1.3314-0.02780.93062.05410.20811.8365-1.02961.7327-60.7563-119.5347-113.0547
372.5081.0169-1.37030.1754-0.38490.5607-0.24690.3234-1.01320.5160.85660.1119-1.89570.77160.00231.38040.2634-0.2180.83280.07421.4323-70.5958-109.8645-119.1491
380.9949-0.5261-0.17060.74680.5650.6392-1.014-0.10680.6804-0.85690.52410.99660.3711-0.4195-0.00031.3444-0.34210.29921.6681-0.03751.5249-76.894-102.6296-99.9263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 168 )
2X-RAY DIFFRACTION2chain 'A' and (resid 169 through 333 )
3X-RAY DIFFRACTION3chain 'A' and (resid 334 through 537 )
4X-RAY DIFFRACTION4chain 'A' and (resid 538 through 806 )
5X-RAY DIFFRACTION5chain 'C' and (resid 25 through 58 )
6X-RAY DIFFRACTION6chain 'C' and (resid 59 through 100 )
7X-RAY DIFFRACTION7chain 'C' and (resid 101 through 127 )
8X-RAY DIFFRACTION8chain 'C' and (resid 128 through 223 )
9X-RAY DIFFRACTION9chain 'C' and (resid 224 through 344 )
10X-RAY DIFFRACTION10chain 'D' and (resid 26 through 119 )
11X-RAY DIFFRACTION11chain 'D' and (resid 120 through 137 )
12X-RAY DIFFRACTION12chain 'D' and (resid 138 through 188 )
13X-RAY DIFFRACTION13chain 'D' and (resid 189 through 243 )
14X-RAY DIFFRACTION14chain 'E' and (resid 24 through 33 )
15X-RAY DIFFRACTION15chain 'E' and (resid 34 through 38 )
16X-RAY DIFFRACTION16chain 'E' and (resid 39 through 58 )
17X-RAY DIFFRACTION17chain 'E' and (resid 59 through 71 )
18X-RAY DIFFRACTION18chain 'E' and (resid 72 through 88 )
19X-RAY DIFFRACTION19chain 'E' and (resid 89 through 110 )
20X-RAY DIFFRACTION20chain 'F' and (resid 25 through 170 )
21X-RAY DIFFRACTION21chain 'F' and (resid 171 through 287 )
22X-RAY DIFFRACTION22chain 'F' and (resid 288 through 807 )
23X-RAY DIFFRACTION23chain 'G' and (resid 28 through 39 )
24X-RAY DIFFRACTION24chain 'G' and (resid 40 through 63 )
25X-RAY DIFFRACTION25chain 'G' and (resid 64 through 83 )
26X-RAY DIFFRACTION26chain 'G' and (resid 84 through 190 )
27X-RAY DIFFRACTION27chain 'G' and (resid 191 through 204 )
28X-RAY DIFFRACTION28chain 'G' and (resid 205 through 213 )
29X-RAY DIFFRACTION29chain 'I' and (resid 24 through 33 )
30X-RAY DIFFRACTION30chain 'I' and (resid 34 through 38 )
31X-RAY DIFFRACTION31chain 'I' and (resid 39 through 58 )
32X-RAY DIFFRACTION32chain 'I' and (resid 59 through 71 )
33X-RAY DIFFRACTION33chain 'I' and (resid 72 through 88 )
34X-RAY DIFFRACTION34chain 'I' and (resid 89 through 110 )
35X-RAY DIFFRACTION35chain 'H' and (resid 26 through 119 )
36X-RAY DIFFRACTION36chain 'H' and (resid 120 through 137 )
37X-RAY DIFFRACTION37chain 'H' and (resid 138 through 188 )
38X-RAY DIFFRACTION38chain 'H' and (resid 189 through 243 )

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