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Yorodumi- PDB-1jrp: Crystal Structure of Xanthine Dehydrogenase inhibited by alloxant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jrp | ||||||
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Title | Crystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter capsulatus | ||||||
Components | (xanthine dehydrogenase, chain ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Partial Beta-Barrel / xdh / xo | ||||||
Function / homology | Function and homology information 1.1.1.204 / xanthine dehydrogenase activity / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Truglio, J.J. / Theis, K. / Leimkuhler, S. / Rappa, R. / Rajagopalan, K.V. / Kisker, C. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Crystal structures of the active and alloxanthine-inhibited forms of xanthine dehydrogenase from Rhodobacter capsulatus Authors: Truglio, J.J. / Theis, K. / Leimkuhler, S. / Rappa, R. / Rajagopalan, K.V. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jrp.cif.gz | 910.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jrp.ent.gz | 733.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jrp_validation.pdf.gz | 969 KB | Display | wwPDB validaton report |
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Full document | 1jrp_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1jrp_validation.xml.gz | 138 KB | Display | |
Data in CIF | 1jrp_validation.cif.gz | 193.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/1jrp ftp://data.pdbj.org/pub/pdb/validation_reports/jr/1jrp | HTTPS FTP |
-Related structure data
Related structure data | 1jroSC S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
-Xanthine dehydrogenase, chain ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 49347.453 Da / Num. of mol.: 4 / Fragment: chain A, residues 1-462 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: EMBL: 2956674, UniProt: O54050*PLUS, 1.1.1.204 #2: Protein | Mass: 82978.031 Da / Num. of mol.: 4 / Fragment: chain B, residues 1-777 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: EMBL: 13397863, UniProt: O54051*PLUS, 1.1.1.204 |
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-Non-polymers , 6 types, 28 molecules
#3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-MTE / #7: Chemical | ChemComp-MOS / #8: Chemical | ChemComp-141 / |
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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: 3.2 Å3/Da / Density % sol: 44 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG, Tris, DTT, isopropanol at pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. all: 135608 / Num. obs: 135608 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1000 / Redundancy: 4.1 % / Rsym value: 0.159 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 3→3.1 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.741 |
Reflection | *PLUS Num. measured all: 551313 / Rmerge(I) obs: 0.159 |
Reflection shell | *PLUS Rmerge(I) obs: 0.741 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JRO Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.867 / SU B: 16.288 / SU ML: 0.31 / SU Rfree: 0.397 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1000 / ESU R Free: 0.397 Details: FOUR-FOLD NCS RESTRAINTS WERE IMPOSED ON CHAINS A, B, C, D AND E, F, G, H
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Solvent computation | Solvent model: BABINET MODEL WITH MAS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.64 Å2
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.077 Å / Total num. of bins used: 20 /
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Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.195 / Rfactor Rfree: 0.244 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.375 / Rfactor Rwork: 0.255 |