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Yorodumi- PDB-1qj9: CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN OMPX FROM ESCHERI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qj9 | ||||||
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Title | CRYSTAL STRUCTURE OF THE OUTER MEMBRANE PROTEIN OMPX FROM ESCHERICHIA COLI | ||||||
Components | OUTER MEMBRANE PROTEIN X | ||||||
Keywords | INTEGRAL MEMBRANE PROTEIN / BETA BARREL / BACTERIAL DEFENSE SYSTEM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å | ||||||
Authors | Vogt, 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 |
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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qj9.cif.gz | 39.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qj9.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/1qj9 ftp://data.pdbj.org/pub/pdb/validation_reports/qj/1qj9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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: MEMBRANEBiological 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 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.1 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9057 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9057 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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
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Displacement parameters | Biso mean: 58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→35 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.233 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |