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- PDB-7jrk: The Structure of BamE from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 7jrk
TitleThe Structure of BamE from Pseudomonas aeruginosa
ComponentsOuter membrane protein assembly factor BamE
KeywordsMEMBRANE PROTEIN / BAM complex / lipoprotein.
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / protein-macromolecule adaptor activity
Similarity search - Function
Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / SmpA / OmlA family / BamE-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Outer membrane protein assembly factor BamE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsBi, M. / Noinaj, N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127884 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM127896 United States
CitationJournal: To Be Published
Title: The crystal structure of BamE from Pseudomonas aeruginosa
Authors: Bi, M. / Noinaj, N.
History
DepositionAug 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein assembly factor BamE
B: Outer membrane protein assembly factor BamE


Theoretical massNumber of molelcules
Total (without water)34,4342
Polymers34,4342
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-37 kcal/mol
Surface area10340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.402, 59.402, 62.104
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Outer membrane protein assembly factor BamE


Mass: 17217.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: bamE, omlA, oprX, PA4765 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O68562
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.84 Å3/Da / Density % sol: 33.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Imidazole, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 26527 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.037 / Rrim(I) all: 0.113 / Χ2: 1.876 / Net I/σ(I): 7.4 / Num. measured all: 253661
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.739.52.60113560.7260.8892.751.035100
1.73-1.769.52.36813030.6040.8142.5061.009100
1.76-1.799.32.28313260.6060.7892.4181.043100
1.79-1.838.91.80113180.750.6421.9131.054100
1.83-1.879.11.45513230.8880.5111.5431.078100
1.87-1.919.11.15513200.9450.4041.2241.139100
1.91-1.969.91.0713570.930.3571.1291.161100
1.96-2.0210.20.73613270.970.2430.7761.257100
2.02-2.0710.10.57313240.990.1910.6051.315100
2.07-2.1410.10.45113390.9870.150.4751.404100
2.14-2.22100.38113050.9870.1270.4021.547100
2.22-2.319.90.27213230.9930.0920.2871.633100
2.31-2.419.70.21613200.9940.0740.2291.904100
2.41-2.5490.15913390.9950.0560.1682.133100
2.54-2.79.20.1313390.9950.0460.1382.381100
2.7-2.919.90.10113220.9980.0350.1072.807100
2.91-3.210.20.08613080.9970.0290.0913.29399.9
3.2-3.669.50.06913430.9970.0250.0743.87499.9
3.66-4.618.30.05713050.9970.0220.0623.66898.5
4.61-509.60.0513300.9980.0180.0532.96899.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WAM

5wam


Resolution: 1.71→29.7 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 46.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1972 7.49 %
Rwork0.2418 24342 -
obs0.2432 26314 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.75 Å2 / Biso mean: 59.7612 Å2 / Biso min: 30.7 Å2
Refinement stepCycle: final / Resolution: 1.71→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 0 67 1446
Biso mean---52.54 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041405
X-RAY DIFFRACTIONf_angle_d0.6861900
X-RAY DIFFRACTIONf_dihedral_angle_d21.193520
X-RAY DIFFRACTIONf_chiral_restr0.047198
X-RAY DIFFRACTIONf_plane_restr0.003263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.71-1.750.53041420.51041724186697
1.75-1.80.47021440.48371745188999
1.8-1.850.51841470.42141719186699
1.85-1.910.43171310.39181736186798
1.91-1.980.48211450.35371726187199
1.98-2.060.31461410.30491726186798
2.06-2.150.36061290.28151755188499
2.15-2.270.3351410.312317351876100
2.27-2.410.30711480.28671722187099
2.41-2.590.27371460.281217691915100
2.59-2.850.32851380.276617491887100
2.85-3.270.27591440.259317361880100
3.27-4.110.19091390.182217551894100
4.12-29.70.17851370.18271745188299

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