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- PDB-9cx4: Acinetobacter baumannii BamA POTRAs 1-4, space group P1 -

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Basic information

Entry
Database: PDB / ID: 9cx4
TitleAcinetobacter baumannii BamA POTRAs 1-4, space group P1
ComponentsOuter membrane protein assembly factor BamA
KeywordsPROTEIN TRANSPORT / membrane protein / transport
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane
Similarity search - Function
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
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / Resolution: 2.78 Å
AuthorsOverly Cottom, C. / Noinaj, N.
Funding support United States, 3items
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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01AI127793 United States
CitationJournal: Structure / Year: 2024
Title: Structural characterization of the POTRA domains from A. baumannii reveals new conformations in BamA.
Authors: Cottom, C.O. / Stephenson, R. / Ricci, D. / Yang, L. / Gumbart, J.C. / Noinaj, N.
History
DepositionJul 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,7592
Polymers74,7592
Non-polymers00
Water59433
1
A: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)37,3801
Polymers37,3801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)37,3801
Polymers37,3801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.524, 61.512, 85.900
Angle α, β, γ (deg.)97.59, 107.34, 112.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Outer membrane protein assembly factor BamA


Mass: 37379.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: yaeT, bamA, ATCC19606_15070 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: A0A6F8TEF0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.37 Å3/Da / Density % sol: 63.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Citric Acid, pH 4.0, and 0.8 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 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: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 23229 / % possible obs: 95.2 % / Redundancy: 2.5 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.105 / Rrim(I) all: 0.181 / Χ2: 1.596 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.78-2.92.41.31623790.2840.6650.9631.6411.05497.6
2.9-3.022.50.99123840.450.7880.7221.2341.07197.9
3.02-3.152.70.72624020.670.8960.510.8921.0598
3.15-3.322.60.47323940.7980.9420.3340.5821.16798
3.32-3.532.60.31623970.8940.9720.2250.391.23697.9
3.53-3.82.50.19223580.950.9870.1390.2381.46796.5
3.8-4.182.30.12122170.9770.9940.0920.1531.70892.3
4.18-4.792.40.0921910.9870.9970.0670.1131.93988.7
4.79-6.032.60.07522230.990.9980.0540.0942.26891.8
6.03-502.50.05422840.9960.9990.0390.0673.28493.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
MOLREP1.19.2-4158phasing
HKL-2000v722data scaling
HKL-20003.27data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→39.37 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2771 1986 8.6 %
Rwork0.2354 --
obs0.239 23090 94.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4934 0 0 33 4967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045027
X-RAY DIFFRACTIONf_angle_d0.6826842
X-RAY DIFFRACTIONf_dihedral_angle_d4.701714
X-RAY DIFFRACTIONf_chiral_restr0.047801
X-RAY DIFFRACTIONf_plane_restr0.005900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.850.4191320.35551398X-RAY DIFFRACTION86
2.85-2.930.38031450.32891542X-RAY DIFFRACTION97
2.93-3.020.35461470.29621551X-RAY DIFFRACTION97
3.02-3.110.32771460.27741556X-RAY DIFFRACTION97
3.11-3.230.30321450.28151554X-RAY DIFFRACTION97
3.23-3.350.34931470.26391560X-RAY DIFFRACTION97
3.35-3.510.27191480.24381577X-RAY DIFFRACTION98
3.51-3.690.28561440.23821528X-RAY DIFFRACTION97
3.69-3.920.31121440.2251532X-RAY DIFFRACTION95
3.92-4.230.24591360.20671444X-RAY DIFFRACTION91
4.23-4.650.24561330.19911418X-RAY DIFFRACTION88
4.65-5.320.27141360.23281440X-RAY DIFFRACTION91
5.32-6.70.27591420.23491518X-RAY DIFFRACTION94
6.7-39.370.21271410.19971486X-RAY DIFFRACTION93

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