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- PDB-1qjp: HIGH RESOLUTION STRUCTURE OF THE OUTER MEMBRANE PROTEIN A (OMPA) ... -

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Basic information

Entry
Database: PDB / ID: 1qjp
TitleHIGH RESOLUTION STRUCTURE OF THE OUTER MEMBRANE PROTEIN A (OMPA) TRANSMEMBRANE DOMAIN
ComponentsOUTER MEMBRANE PROTEIN A
KeywordsOUTER MEMBRANE
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 ...: / 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 / monoatomic ion transmembrane transport / 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 profile. / OmpA-like domain superfamily ...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 profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein A / Outer membrane protein A
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPautsch, A. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: High Resolution Structure of the Ompa Membrane Domain
Authors: Pautsch, A. / Schulz, G.E.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of the Outer Membrane Protein a Transmembrane Domain
Authors: Pautsch, A. / Schulz, G.E.
History
DepositionJun 29, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Advisory / Data collection / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER MEMBRANE PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6347
Polymers18,7961
Non-polymers1,8396
Water1,15364
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.100, 79.700, 50.200
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number5
Space group name H-MC121
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: Protein OUTER MEMBRANE PROTEIN A


Mass: 18795.719 Da / Num. of mol.: 1 / Fragment: TRANSMEMBRANE DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Gene: OMPA / Plasmid: PET3B-171 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02934, UniProt: P0A910*PLUS
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Compound detailsF23L, Q34K AND K107Y WERE INTRODUCED TO OBTAIN XRAY GRADE CRYSTALS

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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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growpH: 5 / Details: 10% PEG 8000, 10 % MPD, 25 MM KH2PO4 PH 5.1
Crystal grow
*PLUS
pH: 4.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.6 %(w/v)C8E41drop
21.4 Mammonium sulfate1reservoir
33.8 %(v/v)2-propanol1reservoir
40.5 %(w/v)C8E41reservoir
51.8 %(w/v)hexyldimethylaminoxide1reservoir
60.1 Mammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 29702 / % possible obs: 95.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.061 / Net I/σ(I): 13.7
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.307 / % possible all: 94.2
Reflection
*PLUS
Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.31

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BXW

1bxw


Resolution: 1.65→12 Å / SU B: 0.60174 / SU ML: 0.02056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.07
Details: THE REGIONS Y18-T30, K64-G70 AND N146-N159 WERE DISORDERED AND ARE NOT INCLUDED IN THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.198 -5 %RANDOM
Rwork0.155 ---
obs-29702 95.4 %-
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 1.65→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 126 64 1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.01
X-RAY DIFFRACTIONp_angle_d0.0370.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0650.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it6.8232
X-RAY DIFFRACTIONp_mcangle_it9.2043
X-RAY DIFFRACTIONp_scbond_it7.7422
X-RAY DIFFRACTIONp_scangle_it10.1973
X-RAY DIFFRACTIONp_plane_restr0.0245
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.2350.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1730.3
X-RAY DIFFRACTIONp_planar_tor4.23
X-RAY DIFFRACTIONp_staggered_tor14.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.5

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