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- PDB-1bxw: OUTER MEMBRANE PROTEIN A (OMPA) TRANSMEMBRANE DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1bxw
TitleOUTER MEMBRANE PROTEIN A (OMPA) TRANSMEMBRANE DOMAIN
ComponentsPROTEIN (OUTER MEMBRANE PROTEIN A)
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE / TRANSMEMBRANE PROTEIN
Function / homology
Function and homology information


outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / cell outer membrane / outer membrane-bounded periplasmic space / symbiont entry into host cell ...outer membrane protein complex / monoatomic ion transmembrane transporter activity / detection of virus / outer membrane / porin activity / pore complex / monoatomic ion transport / cell outer membrane / outer membrane-bounded periplasmic space / symbiont entry into host cell / DNA damage response / identical protein binding / membrane
Similarity search - Function
Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Porin - #20 / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain ...Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Porin - #20 / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein A
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.5 Å
AuthorsSchulz, G.E. / Pautsch, A.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structure of the outer membrane protein A transmembrane domain.
Authors: Pautsch, A. / Schulz, G.E.
History
DepositionOct 3, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Feb 15, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (OUTER MEMBRANE PROTEIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1992
Polymers18,8931
Non-polymers3061
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.180, 77.950, 50.930
Angle α, β, γ (deg.)90.00, 91.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (OUTER MEMBRANE PROTEIN A)


Mass: 18892.898 Da / Num. of mol.: 1 / Fragment: TRANSMEMBRANE DOMAIN / Mutation: F23L, Q34K, K107Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Species: Escherichia coli / Strain: BL21DE3 / Gene: OMPA / Plasmid: PET3B-171 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P0A910
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.7 Å3/Da / Density % sol: 66.7 %
Crystal growpH: 5
Details: 10 % PEG-8000 10 % MPD 0.05 M POTASSIUM PHOSPHATE PH 5.0
Crystal grow
*PLUS
pH: 5.1 / Method: vapor diffusion, hanging drop
Details: drop contained 1:1 mixture of protein and reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.6 %(w/v)1dropC8E4
312 %(w/v)PEG80001reservoir
410 %(v/v)MPD1reservoir
525 mM1reservoirKH2PO4

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 15, 1998
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8328 / % possible obs: 89 % / Redundancy: 2.1 % / Biso Wilson estimate: 49.2 Å2 / Rsym value: 0.028 / Net I/σ(I): 16.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 1.2 % / Mean I/σ(I) obs: 6.6 / Rsym value: 0.11 / % possible all: 53
Reflection
*PLUS
Rmerge(I) obs: 0.028
Reflection shell
*PLUS
% possible obs: 53 % / Rmerge(I) obs: 0.11

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Processing

Software
NameVersionClassification
SHARPphasing
REFMACrefinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→50 Å / SU B: 3.64 / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED REGIONS ARE FROM GLY22-GLY28, GLY65-GLU68 AND ILE147-PRO147 WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.235 404 5 %RANDOM
Rwork0.189 ---
obs-8328 89 %-
Displacement parametersBiso mean: 60.4 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 21 39 1390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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