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Yorodumi- PDB-4qq3: Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, dele... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qq3 | ||||||
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Title | Inosine 5'-monophosphate dehydrogenase from Vibrio cholerae, deletion mutant, in complex with XMP | ||||||
Components | Inosine-5'-monophosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / STRUCTURAL GENOMICS / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID | ||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Osipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Inosine 5'-monophosphate dehydrogenase from vibrio cholerae, deletion mutant, in complex with xmp Authors: Osipiuk, J. / Maltseva, N. / Makowska-Grzyska, M. / Gu, M. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qq3.cif.gz | 136.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qq3.ent.gz | 103.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/4qq3 ftp://data.pdbj.org/pub/pdb/validation_reports/qq/4qq3 | HTTPS FTP |
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-Related structure data
Related structure data | 4qneS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | based on PISA |
-Components
#1: Protein | Mass: 38247.703 Da / Num. of mol.: 1 / Fragment: UNP residues 220-489 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: guaB, VC0767, VC_0767 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KTW3, IMP dehydrogenase | ||||
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#2: Chemical | ChemComp-XMP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | RESIDUES 91-219 ARE DELETED AND REPLACED WITH AN SGG LINKER. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% PEG 2000, 19.3% PEG 200, 0.05 M Tris-buffer, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 23, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.72→38.6 Å / Num. all: 40250 / Num. obs: 40250 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 33.7 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.34 / Net I/σ(I): 12.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QNE Resolution: 1.72→38.6 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.078 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.087 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 109.69 Å2 / Biso mean: 35.722 Å2 / Biso min: 14.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→38.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.765 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -2.1544 Å / Origin y: 24.2778 Å / Origin z: 16.9284 Å
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