+Open data
-Basic information
Entry | Database: PDB / ID: 2vix | ||||||
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Title | Methylated Shigella flexneri MxiC | ||||||
Components | PROTEIN MXIC | ||||||
Keywords | TRANSPORT PROTEIN / SECRETION REGULATION / T3SS / VIRULENCE / 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: 2.85 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 | 2vix.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vix.ent.gz | 155.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vix_validation.pdf.gz | 498.6 KB | Display | wwPDB validaton report |
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Full document | 2vix_full_validation.pdf.gz | 528.9 KB | Display | |
Data in XML | 2vix_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 2vix_validation.cif.gz | 48.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/2vix ftp://data.pdbj.org/pub/pdb/validation_reports/vi/2vix | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 34184.215 Da / Num. of mol.: 3 / 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: Chemical | ChemComp-ACT / | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | N-DIMETHYL-LYSINE (MLY): GENERATED FOLLOWING THE METHYLATION PROTOCOL DESCRIBED IN WALTERS ET AL. ...N-DIMETHYL-LYSINE (MLY): GENERATED FOLLOWING THE METHYLATIO | 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: 2.95 Å3/Da / Density % sol: 58.4 % Description: THE SEARCH MODEL WAS A LOW-RESOLUTION MODEL TRACED IN THE DENSITY FROM A SEMET CRYSTAL |
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Crystal grow | pH: 7.5 Details: 0.2M NAACETATE, 0.1 BISTRIS PROPANE PH 7.5, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9757 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 4, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9757 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50.4 Å / Num. obs: 84697 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 65.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.4 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→50.4 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: REFINED IN BUSTER-TNT VERSION 2.1.1 WITH RESTRAINTS FROM A MODEL REFINED IN REFMAC5
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 60 Å2 / ksol: 0.211 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→50.4 Å
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Refine LS restraints |
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