+Open data
-Basic information
Entry | Database: PDB / ID: 2ivm | ||||||
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Title | Crystal structure of a transcriptional regulator | ||||||
Components | TRANSCRIPTIONAL REGULATORY PROTEIN | ||||||
Keywords | TRANSCRIPTION / TRANSCRIPTIONAL REGULATOR | ||||||
Function / homology | Function and homology information amino acid binding / response to amino acid / protein homooligomerization / sequence-specific DNA binding / DNA binding / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.5 Å | ||||||
Authors | Shrivastava, T. / Ramachandran, R. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2007 Title: Mechanistic Insights from the Crystal Structures of a Feast/Famine Regulatory Protein from Mycobacterium Tuberculosis H37Rv. Authors: Shrivastava, T. / Ramachandran, R. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED 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 | 2ivm.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ivm.ent.gz | 51 KB | Display | PDB format |
PDBx/mmJSON format | 2ivm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ivm_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 2ivm_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 2ivm_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 2ivm_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/2ivm ftp://data.pdbj.org/pub/pdb/validation_reports/iv/2ivm | HTTPS FTP |
-Related structure data
Related structure data | 2vbwC 2vbxC 2vbyC 2vbzC 2vc0C 2vc1C 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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Unit cell |
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-Components
#1: Protein | Mass: 16516.570 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96896 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | A22G MUTATION INTRODUCED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.73 % |
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Crystal grow | pH: 6.5 / Details: pH 6.5 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 18352 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.5→30.07 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.57 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30.07 Å
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Refine LS restraints |
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