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Yorodumi- PDB-2w54: Crystal Structure of Xanthine Dehydrogenase from Rhodobacter caps... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w54 | ||||||
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Title | Crystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus in Complex with Bound Inhibitor Pterin-6-aldehyde | ||||||
Components | (XANTHINE DEHYDROGENASE) x 2 | ||||||
Keywords | OXIDOREDUCTASE / XANTHINE OXIDASE / PURINE CATABOLISM / P6A / IRON / IRON-SULFUR / METAL-BINDING / MOLYBDENUM COFACTOR | ||||||
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: 3.3 Å | ||||||
Authors | Doebbler, J.A. / Truglio, J.J. / Leimkuhler, S. / Kisker, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Mechanism of Substrate and Inhibitor Binding of Rhodobacter Capsulatus Xanthine Dehydrogenase. Authors: Dietzel, U. / Kuper, J. / Doebbler, J.A. / Schulte, A. / Truglio, J.J. / Leimkuhler, S. / Kisker, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w54.cif.gz | 877.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w54.ent.gz | 708.5 KB | Display | PDB format |
PDBx/mmJSON format | 2w54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/2w54 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/2w54 | HTTPS FTP |
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-Related structure data
Related structure data | 2w3rC 2w3sC 2w55C 1jroS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
NCS oper:
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-Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 49420.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Plasmid: PSL207 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: O54050, 1.1.1.204 #2: Protein | Mass: 82978.031 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Plasmid: PSL207 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: O54051, 1.1.1.204 |
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-Non-polymers , 5 types, 24 molecules
#3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-XAX / {[( #6: Chemical | ChemComp-BA / #7: Chemical | ChemComp-HHR / |
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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: 3.35 Å3/Da / Density % sol: 63.26 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.3 Details: 100 MM TRIS PH 8.3, 6-8 % PEG 8000, 6-8 MM BACL, 5-25 MM DTT, 3-4 % ISOPROPANOL, 10-15 MG/ML PROTEIN, HANGING DROP VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Details: A DOUBLY FOCUSING TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 102161 / % possible obs: 99.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JRO Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.877 / SU B: 43.602 / SU ML: 0.33 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.23 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
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Refine LS restraints |
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