+Open data
-Basic information
Entry | Database: PDB / ID: 2vj4 | ||||||
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Title | Methylated Shigella flexneri MxiC | ||||||
Components | PROTEIN MXIC | ||||||
Keywords | TRANSPORT PROTEIN / SECRETION REGULATION / T3SS / VIRULENCE / TRANSPORT / TYPE THREE SECRETION SYSTEM | ||||||
Function / homology | Function and homology information protein secretion by the type III secretion system / outer membrane / negative regulation of protein secretion / host cell / cell surface / extracellular region Similarity search - Function | ||||||
Biological species | SHIGELLA FLEXNERI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Deane, J.E. / Roversi, P. / King, C. / Johnson, S. / Lea, S.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structures of the Shigella Flexneri Type 3 Secretion System Protein Mxic Reveal Conformational Variability Amongst Homologues. Authors: Deane, J.E. / Roversi, P. / King, C. / Johnson, S. / Lea, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vj4.cif.gz | 134.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vj4.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vj4_validation.pdf.gz | 454.7 KB | Display | wwPDB validaton report |
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Full document | 2vj4_full_validation.pdf.gz | 485 KB | Display | |
Data in XML | 2vj4_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 2vj4_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vj4 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vj4 | HTTPS FTP |
-Related structure data
Related structure data | 2vixSC 2vj5C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.00049, 1, 0.00076), Vector: |
-Components
#1: Protein | Mass: 34184.215 Da / Num. of mol.: 2 / Fragment: RESIDUES 74-355 Source method: isolated from a genetically manipulated source Details: THE CONSTRUCT IS A DELETION OF THE FIRST 73 RESIDUES AND WAS METHYLATED CHEMICALLY FOLLOWING WALTER ET AL, STRUCTURE 14,1617-1622 (2006) Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: PWR100 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04640 #2: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT IS A DELETION OF RESIDUES 1-73 AND THEN HAS THE SEQUENCE HSSGLVPRGSHM FROM THE ...THE CONSTRUCT IS A DELETION OF RESIDUES 1-73 AND THEN HAS THE SEQUENCE HSSGLVPRGS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62 % / Description: NONE |
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Crystal grow | pH: 7 Details: 1.0 M SUCCINIC ACID, 0.1 M HEPES PH 7.0, 1% W/V PEGMME 2000 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 22, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→42 Å / Num. obs: 28754 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 59.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VIX Resolution: 2.5→42 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: REFINED IN BUSTER-TNT VERSION 2.1.1 WITH RESTRAINTS BASED ON REFMAC5 THE LATTICE IS PSEUDOTETRAGONAL P 42 2 2 BUT REFINEMENT IN THIS SPACE GROUP WITH 1 MOL PER ASU DID NOT WORK WELL
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Refinement step | Cycle: LAST / Resolution: 2.5→42 Å
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Refine LS restraints |
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