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- PDB-1qj8: CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN OMPX FROM ESCHERI... -

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Basic information

Entry
Database: PDB / ID: 1qj8
TitleCRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN OMPX FROM ESCHERICHIA COLI
ComponentsOUTER MEMBRANE PROTEIN X
KeywordsMEMBRANE PROTEIN / BETA-BARREL / BACTERIAL DEFENSE SYSTEM / PLATINUM COMPLEX STRUCTURE
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
PLATINUM(II) DI-CHLORIDE / Outer membrane protein X / Outer membrane protein X
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsVogt, J. / Schulz, G.E.
Citation
Journal: Structure / Year: 1999
Title: The Structure of the Outer Membrane Protein Ompx from Escherichia Coli Reveals Mechanisms of Virulence
Authors: Vogt, J. / Schulz, G.E.
#1: Journal: Proteins / 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 10, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2104
Polymers16,3721
Non-polymers8383
Water1,29772
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.400, 82.400, 206.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

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Components

#1: Protein OUTER MEMBRANE PROTEIN X


Mass: 16371.768 Da / Num. of mol.: 1 / Mutation: YES
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: 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: Chemical ChemComp-PCL / PLATINUM(II) DI-CHLORIDE


Mass: 265.984 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl2Pt
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 123 TO ASN

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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: 1.9→34 Å / Num. obs: 20466 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.061 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.274 / % possible all: 92
Reflection
*PLUS
Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Rmerge(I) obs: 0.27

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→34 Å / SU B: 1.539 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1037 5 %RANDOM
Rwork0.204 ---
obs-20466 95 %-
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 25 72 1255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.034
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: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS

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