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Yorodumi- PDB-3dms: 1.65A crystal structure of isocitrate dehydrogenase from Burkhold... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dms | ||||||
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Title | 1.65A crystal structure of isocitrate dehydrogenase from Burkholderia pseudomallei | ||||||
Components | Isocitrate dehydrogenase [NADP] | ||||||
Keywords | OXIDOREDUCTASE / BURKHOLDERIA / PSEUDOMALLEI / ISOCITRATE / DEHYDROGENASE / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / Glyoxylate bypass / Manganese / Metal-binding / NADP / Tricarboxylic acid cycle | ||||||
Function / homology | Function and homology information isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / NAD binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Structural basis of the substrate specificity of bifunctional isocitrate dehydrogenase kinase/phosphatase. Authors: Yates, S.P. / Edwards, T.E. / Bryan, C.M. / Stein, A.J. / Van Voorhis, W.C. / Myler, P.J. / Stewart, L.J. / Zheng, J. / Jia, Z. #1: Journal: Plos One / Year: 2013 Title: Combining functional and structural genomics to sample the essential Burkholderia structome. Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dms.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dms.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/3dms ftp://data.pdbj.org/pub/pdb/validation_reports/dm/3dms | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47231.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710B / Gene: icd, BPSL0896 / Plasmid: BG1861rc / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q63WJ4, UniProt: Q3JV82*PLUS, isocitrate dehydrogenase (NADP+) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.45 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 7 Details: 20% PEG 3350, 2M POTASSIUM FORMATE, pH 7, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→45.68 Å / Num. obs: 47920 / % possible obs: 99.8 % / Redundancy: 3.35 % / Rmerge(I) obs: 0.043 / Χ2: 0.96 / Net I/σ(I): 13.9 / Scaling rejects: 403 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 27.69 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→45.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.827 / SU B: 2.353 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.11 / 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 max: 47.09 Å2 / Biso mean: 23.227 Å2 / Biso min: 12.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→45.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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