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- PDB-5or1: BamA structure of Salmonella enterica -

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Basic information

Entry
Database: PDB / ID: 5or1
TitleBamA structure of Salmonella enterica
ComponentsOuter membrane protein assembly factor BamA
KeywordsMEMBRANE PROTEIN / Outer membrane protein
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane
Similarity search - Function
membrane protein fhac: a member of the omp85/tpsb transporter family / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin ...membrane protein fhac: a member of the omp85/tpsb transporter family / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsDong, C. / Gu, Y.
CitationJournal: Biochem. J. / Year: 2017
Title: BamA beta 16C strand and periplasmic turns are critical for outer membrane protein insertion and assembly.
Authors: Gu, Y. / Zeng, Y. / Wang, Z. / Dong, C.
History
DepositionAug 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 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

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)89,6171
Polymers89,6171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.037, 124.037, 131.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Outer membrane protein assembly factor BamA


Mass: 89617.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: bamA, yaeT, STM0224
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8ZRP0

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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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES sodium (pH 7.5) and 1.0 M sodium citrate tribasic dehydrate

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Data collection

DiffractionMean temperature: 146 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.92→130 Å / Num. obs: 13411 / % possible obs: 100 % / Redundancy: 17.3 % / Net I/σ(I): 7.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.92→107.42 Å / Cor.coef. Fo:Fc: 0.855 / Cor.coef. Fo:Fc free: 0.874 / SU B: 20.586 / SU ML: 0.397 / Cross valid method: THROUGHOUT / ESU R: 1.524 / ESU R Free: 0.494 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34703 666 4.9 %RANDOM
Rwork0.30684 ---
obs0.30884 12829 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.624 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20.68 Å20 Å2
2--1.37 Å20 Å2
3----4.44 Å2
Refinement stepCycle: 1 / Resolution: 2.92→107.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 0 0 2944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023028
X-RAY DIFFRACTIONr_bond_other_d0.0020.022521
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9254121
X-RAY DIFFRACTIONr_angle_other_deg1.1135873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7625379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21824.803152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.77315432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2311510
X-RAY DIFFRACTIONr_chiral_restr0.1330.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213514
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02672
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.4129.0571519
X-RAY DIFFRACTIONr_mcbond_other4.4099.0571518
X-RAY DIFFRACTIONr_mcangle_it7.45513.5851897
X-RAY DIFFRACTIONr_mcangle_other7.45413.5861898
X-RAY DIFFRACTIONr_scbond_it3.429.1921506
X-RAY DIFFRACTIONr_scbond_other3.4199.1921507
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.89613.7372224
X-RAY DIFFRACTIONr_long_range_B_refined11.3673433
X-RAY DIFFRACTIONr_long_range_B_other11.3663434
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.919→2.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 48 -
Rwork0.487 923 -
obs--99.9 %

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