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- PDB-3q6b: The high-resolution and new form crystal structure of BamA POTRA4... -

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Basic information

Entry
Database: PDB / ID: 3q6b
TitleThe high-resolution and new form crystal structure of BamA POTRA4-5 from E.coli
ComponentsOuter membrane protein assembly complex, YaeT protein
KeywordsPROTEIN BINDING / POTRA FOLD / INSERTION OF OUTER MEMBRANE PROTEINS
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
Similarity search - Function
membrane protein fhac / 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 / Ubiquitin-like (UB roll) ...membrane protein fhac / 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 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
: / Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGao, Z.Q. / Zhang, H. / Dong, Y.H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: High-resolution structure of a new crystal form of BamA POTRA4-5 from Escherichia coli.
Authors: Zhang, H. / Gao, Z.Q. / Hou, H.F. / Xu, J.H. / Li, L.F. / Su, X.D. / Dong, Y.H.
History
DepositionDec 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein assembly complex, YaeT protein


Theoretical massNumber of molelcules
Total (without water)21,3541
Polymers21,3541
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.530, 39.005, 32.561
Angle α, β, γ (deg.)90.00, 101.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Outer membrane protein assembly complex, YaeT protein


Mass: 21353.914 Da / Num. of mol.: 1 / Fragment: POTRA45 DOMAIN (UNP RESIDUES 266-420)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: EcDH1_3426, YAET / Plasmid: pet-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9QRL1, UniProt: P0A940*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium acetate, 0.1M Sodium cacodylate pH 6.5, 30% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 26711 / Num. obs: 25465 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.336 / Num. unique all: 2260 / % possible all: 83.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3OG5

3og5


Resolution: 1.5→25.794 Å / SU ML: 0.15 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 1294 5.06 %RANDOM
Rwork0.1466 ---
all0.1466 26711 --
obs0.1487 25465 92.9 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.232 Å2 / ksol: 0.419 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2862 Å2-0 Å2-0.2229 Å2
2---1.5807 Å2-0 Å2
3---1.2945 Å2
Refinement stepCycle: LAST / Resolution: 1.5→25.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 0 141 1377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051306
X-RAY DIFFRACTIONf_angle_d0.9381766
X-RAY DIFFRACTIONf_dihedral_angle_d12.614525
X-RAY DIFFRACTIONf_chiral_restr0.057190
X-RAY DIFFRACTIONf_plane_restr0.003236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.5570.30681030.2007200870
1.557-1.62790.20551290.1435254188
1.6279-1.71370.20051220.1269267292
1.7137-1.8210.16531370.1119272694
1.821-1.96160.16481580.1154277597
1.9616-2.15890.18151780.1241285899
2.1589-2.47110.1881490.13292872100
2.4711-3.11240.18951600.15232916100
3.1124-25.79750.18861580.1682289897

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