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- PDB-1qj9: CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN OMPX FROM ESCHERI... -

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Basic information

Entry
Database: PDB / ID: 1qj9
TitleCRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN OMPX FROM ESCHERICHIA COLI
ComponentsOUTER MEMBRANE PROTEIN X
KeywordsINTEGRAL MEMBRANE PROTEIN / BETA BARREL / BACTERIAL DEFENSE SYSTEM
Function / homology
Function and homology information


host outer membrane / membrane => GO:0016020 / cell outer membrane
Similarity search - Function
: / Enterobacterial virulence outer membrane protein signature 1. / Virulence-related outer membrane protein / Enterobacterial virulence outer membrane protein signature 2. / Outer membrane protein beta-barrel domain / Outer membrane protein beta-barrel domain / Porin - #20 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein X / Outer membrane protein X
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsVogt, J. / Schulz, G.E.
Citation
Journal: Structure / Year: 1999
Title: The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence.
Authors: Vogt, J. / Schulz, G.E.
#1: Journal: Proteins: Struct.,Funct., Genet. / Year: 1999
Title: Strategy for Membrane Protein Crystallization Exemplified with Ompa and Ompx
Authors: Pautsch, A. / Vogt, J. / Model, K. / Siebold, C. / Schulz, G.E.
History
DepositionJun 23, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 16, 2019Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 6, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.5Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / pdbx_database_status
Item: _citation.pdbx_database_id_DOI / _pdbx_database_status.status_code_sf
Revision 1.8May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEET PRESENTED AS "A" ON SHEET RECORDS BELOW IS ACTUALLY AN ... SHEET DETERMINATION METHOD: DSSP THE SHEET PRESENTED AS "A" ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER MEMBRANE PROTEIN X


Theoretical massNumber of molelcules
Total (without water)16,3721
Polymers16,3721
Non-polymers00
Water1,20767
1
A: OUTER MEMBRANE PROTEIN X
x 6


Theoretical massNumber of molelcules
Total (without water)98,2316
Polymers98,2316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Unit cell
Length a, b, c (Å)82.300, 82.300, 208.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein OUTER MEMBRANE PROTEIN X


Mass: 16371.768 Da / Num. of mol.: 1 / Mutation: H100N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: MEMBRANE / Gene: OMPX / Plasmid: PET3B / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36546, UniProt: P0A917*PLUS
#2: Water ChemComp-HOH / 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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growpH: 4.6
Details: 30 % (V/V) 2-PROPANOL, 20 % (V/V) GLYCEROL, 0.2 M CACL2, 0.1 M NA-ACETATE PH 4.6
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %(v/v)2-propanol1reservoir
220 %(v/v)glycerol1reservoir
30.2 M1reservoirCaCl2
40.1 Msodium acetate1reservoir
520 mg/mlprotain1drop
60.6 %(v/v)1dropC8E4
720 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9057
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9057 Å / Relative weight: 1
ReflectionResolution: 2.1→35 Å / Num. obs: 16165 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 42 Å2 / Rsym value: 0.076 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.317 / % possible all: 99
Reflection
*PLUS
Rmerge(I) obs: 0.076
Reflection shell
*PLUS
Rmerge(I) obs: 0.32

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→35 Å / SU B: 2.2 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.284 809 5 %RANDOM
Rwork0.233 ---
obs-16165 99 %-
Displacement parametersBiso mean: 58 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 0 67 1225
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d0.041
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
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS

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