+Open data
-Basic information
Entry | Database: PDB / ID: 3jv9 | ||||||
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Title | The structure of a reduced form of OxyR from N. meningitidis | ||||||
Components | Transcriptional regulator, LysR family | ||||||
Keywords | TRANSCRIPTION / LysR-type transcriptional regulator / LTTR / redox / Structural Genomics / OPPF / Oxford Protein Production Facility / DNA-binding / Transcription regulation / OPPF3291 | ||||||
Function / homology | Function and homology information cis-regulatory region sequence-specific DNA binding => GO:0000987 / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.39 Å | ||||||
Authors | Sainsbury, S. / Ren, J. / Stuart, D.I. / Owens, R.J. / Oxford Protein Production Facility (OPPF) | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2010 Title: The structure of a reduced form of OxyR from Neisseria meningitidis Authors: Sainsbury, S. / Ren, J. / Nettleship, J.E. / Saunders, N.J. / Stuart, D.I. / Owens, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jv9.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jv9.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 3jv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jv9_validation.pdf.gz | 434.8 KB | Display | wwPDB validaton report |
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Full document | 3jv9_full_validation.pdf.gz | 456.5 KB | Display | |
Data in XML | 3jv9_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 3jv9_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/3jv9 ftp://data.pdbj.org/pub/pdb/validation_reports/jv/3jv9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 24593.312 Da / Num. of mol.: 2 / Fragment: residues 88-306 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0173 / Plasmid: OPPF3291 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9K1H8 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.23 Å3/Da / Density % sol: 44.79 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 20% PEG 3350, 0.2M calcium acetate, 0.2mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785, 0.9070 | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2006 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.39→30 Å / Num. obs: 16661 / % possible obs: 96.8 % / Observed criterion σ(I): -1.5 / Redundancy: 6.9 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 18.4 | |||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1280 / % possible all: 76.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.39→29.798 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.671 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 36.06 / Stereochemistry target values: ML Details: ANOMALOUS SCATTERER GROUPS DETAILS. NUMBER OF ANOMALOUS SCATTERER GROUPS : 1 ANOMALOUS SCATTERER GROUP : 1 SELECTION: name SE FP : -3.9200 FDP : 5.8667
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.489 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 276.97 Å2 / Biso mean: 53.436 Å2 / Biso min: 20.69 Å2
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Refinement step | Cycle: LAST / Resolution: 2.39→29.798 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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