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- PDB-4n75: Structural Basis of BamA-mediate Outer Membrane Protein Biogenesis -

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Basic information

Entry
Database: PDB / ID: 4n75
TitleStructural Basis of BamA-mediate Outer Membrane Protein Biogenesis
ComponentsOuter membrane protein assembly factor BamA
KeywordsMEMBRANE PROTEIN / barrel / Outer Membrane Protein Biogenesis / OMP85 / yaet
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: a member of the omp85/tpsb transporter family / 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 / 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 / POTRA domain / POTRA domain profile. / Surface antigen D15-like / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å
AuthorsNi, D.C.
CitationJournal: Faseb J. / Year: 2014
Title: Structural and functional analysis of the beta-barrel domain of BamA from Escherichia coli.
Authors: Ni, D. / Wang, Y. / Yang, X. / Zhou, H. / Hou, X. / Cao, B. / Lu, Z. / Zhao, X. / Yang, K. / Huang, Y.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)86,0712
Polymers86,0712
Non-polymers00
Water57632
1
A: Outer membrane protein assembly factor BamA


Theoretical massNumber of molelcules
Total (without water)43,0361
Polymers43,0361
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)43,0361
Polymers43,0361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.492, 159.883, 56.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A
21CHAIN B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TRP / End label comp-ID: TRP / Auth seq-ID: 426 - 810 / Label seq-ID: 1 - 385

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN AAA
2CHAIN BBB

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Components

#1: Protein Outer membrane protein assembly factor BamA / Omp85


Mass: 43035.734 Da / Num. of mol.: 2 / Fragment: barrel domain, UNP residues 427-810
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655 / Plasmid: pet24A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P0A940
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES PH 6.0, 6% Tacsimate, 25% PEG 4000, 0.6% C8E4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.604→50 Å / Num. obs: 31883 / % possible obs: 93.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.3 % / Biso Wilson estimate: 51.52 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.6-3.45196.7
3.45-3.66195.3
3.66-3.97195.2
3.97-4.34194
4.97-6.26193.6
6.26-35.27188.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K3C

4k3c


Resolution: 2.604→36.268 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7922 / SU ML: 0.35 / σ(F): 1.34 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 1997 6.28 %RANDOM
Rwork0.205 ---
all0.247 ---
obs0.2081 31820 95.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.75 Å2 / Biso mean: 51.8867 Å2 / Biso min: 13.44 Å2
Refinement stepCycle: LAST / Resolution: 2.604→36.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5858 0 0 32 5890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016041
X-RAY DIFFRACTIONf_angle_d1.4218227
X-RAY DIFFRACTIONf_dihedral_angle_d16.0942079
X-RAY DIFFRACTIONf_chiral_restr0.058828
X-RAY DIFFRACTIONf_plane_restr0.0071083
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3182X-RAY DIFFRACTION12.824TORSIONAL
12B3182X-RAY DIFFRACTION12.824TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6038-2.66890.34621390.27362075221494
2.6689-2.7410.36771420.27162123226597
2.741-2.82170.32121420.24972139228197
2.8217-2.91270.33491450.22752149229497
2.9127-3.01680.28961410.21612119226097
3.0168-3.13750.29031450.2292157230297
3.1375-3.28020.27391430.20762127227096
3.2802-3.4530.25881430.20812124226796
3.453-3.66910.26061420.19152122226496
3.6691-3.95210.22281430.1872139228295
3.9521-4.34920.25381430.18872136227995
4.3492-4.97720.19111410.16282124226594
4.9772-6.26550.21091450.20032161230694
6.2655-36.27140.24981430.23082128227189
Refinement TLS params.Method: refined / Origin x: 44.0671 Å / Origin y: 40.6857 Å / Origin z: 17.6839 Å
111213212223313233
T0.1231 Å2-0.0131 Å20.0093 Å2-0.1857 Å2-0.001 Å2--0.1855 Å2
L0.3049 °20.001 °2-0.0513 °2-0.0754 °2-0.0523 °2--1.1738 °2
S0.0829 Å °0.0762 Å °0.0084 Å °-0.0309 Å °-0.059 Å °-0.0216 Å °-0.0331 Å °-0.0264 Å °-0.0006 Å °
Refinement TLS groupSelection details: ALL

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