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- PDB-4xga: Crystal structure of BamB and BamA P3-5 complex from E.coli -

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Basic information

Entry
Database: PDB / ID: 4xga
TitleCrystal structure of BamB and BamA P3-5 complex from E.coli
Components
  • Outer membrane protein assembly factor BamA
  • Outer membrane protein assembly factor BamB
KeywordsPROTEIN BINDING/MEMBRANE PROTEIN / outer member protein / PROTEIN BINDING-MEMBRANE PROTEIN complex
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / cell adhesion / membrane / identical protein binding
Similarity search - Function
membrane protein fhac / PQQ enzyme repeat / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamA / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. ...membrane protein fhac / PQQ enzyme repeat / Outer membrane protein assembly factor BamB / Outer membrane protein assembly factor BamA / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Quinoprotein alcohol dehydrogenase-like superfamily / Ubiquitin-like (UB roll) / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChen, Z. / Zhan, L.H. / Dong, C. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural basis for the interaction of BamB with the POTRA3-4 domains of BamA.
Authors: Chen, Z. / Zhan, L.H. / Hou, H.F. / Gao, Z.Q. / Xu, J.H. / Dong, C. / Dong, Y.H.
History
DepositionDec 30, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamB
B: Outer membrane protein assembly factor BamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0653
Polymers68,0252
Non-polymers401
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-20 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.035, 109.642, 49.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Outer membrane protein assembly factor BamB


Mass: 39882.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamB, yfgL, b2512, JW2496 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77774
#2: Protein Outer membrane protein assembly factor BamA / Omp85


Mass: 28142.543 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 175-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bamA, yaeT, yzzN, yzzY, b0177, JW0172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A940
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% w/v Tryptone, 20% w/v Polyethylene glycol 3350, 0.05M HEPES sodium pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 15, 2014
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 33219 / Num. obs: 33219 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 29.43 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.8
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q54, 3q6b

3q54

3q6b


Resolution: 2.15→30.357 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1679 5.06 %random
Rwork0.1808 33165 --
obs0.1833 33165 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→30.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4003 0 1 279 4283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084074
X-RAY DIFFRACTIONf_angle_d1.165540
X-RAY DIFFRACTIONf_dihedral_angle_d14.5511461
X-RAY DIFFRACTIONf_chiral_restr0.046635
X-RAY DIFFRACTIONf_plane_restr0.005720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20770.28431450.21832441X-RAY DIFFRACTION96
2.2077-2.2790.24571380.19622607X-RAY DIFFRACTION100
2.279-2.36040.25331330.19142611X-RAY DIFFRACTION100
2.3604-2.45490.25611280.18932604X-RAY DIFFRACTION100
2.4549-2.56650.25581430.19052573X-RAY DIFFRACTION100
2.5665-2.70180.26751380.19782614X-RAY DIFFRACTION100
2.7018-2.87090.2561340.2012641X-RAY DIFFRACTION100
2.8709-3.09240.2471660.20292593X-RAY DIFFRACTION100
3.0924-3.40320.23581440.18992629X-RAY DIFFRACTION100
3.4032-3.89480.22511340.1742666X-RAY DIFFRACTION100
3.8948-4.90370.19821320.14982696X-RAY DIFFRACTION100
4.9037-30.36010.19391440.16942811X-RAY DIFFRACTION99

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