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Yorodumi- PDB-2c6z: crystal structure of dimethylarginine dimethylaminohydrolase I in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c6z | |||||||||
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Title | crystal structure of dimethylarginine dimethylaminohydrolase I in complex with citrulline | |||||||||
Components | NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1 | |||||||||
Keywords | HYDROLASE / DDAH I / NO / NOS / ADMA / MMA / ACETYLATION / METAL-BINDING / S-NITROSYLATION / ZINC | |||||||||
Function / homology | Function and homology information protein nitrosylation / eNOS activation / dimethylargininase / dimethylargininase activity / citrulline metabolic process / arginine metabolic process / amino acid binding / nitric oxide biosynthetic process / positive regulation of nitric oxide biosynthetic process / zinc ion binding Similarity search - Function | |||||||||
Biological species | BOS TAURUS (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | |||||||||
Authors | Frey, D. / Braun, O. / Briand, C. / Vasak, M. / Grutter, M.G. | |||||||||
Citation | Journal: Structure / Year: 2006 Title: Structure of the Mammalian Nos Regulator Dimethylarginine Dimethylaminohydrolase: A Basis for the Design of Specific Inbitors Authors: Frey, D. / Braun, O. / Briand, C. / Vasak, M. / Grutter, M.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c6z.cif.gz | 143.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c6z.ent.gz | 111.3 KB | Display | PDB format |
PDBx/mmJSON format | 2c6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c6z_validation.pdf.gz | 354.4 KB | Display | wwPDB validaton report |
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Full document | 2c6z_full_validation.pdf.gz | 354.3 KB | Display | |
Data in XML | 2c6z_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 2c6z_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/2c6z ftp://data.pdbj.org/pub/pdb/validation_reports/c6/2c6z | HTTPS FTP |
-Related structure data
Related structure data | 2ci1C 2ci3C 2ci4C 2ci5C 2ci6C 2ci7C 1h70S 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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Unit cell |
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-Components
#1: Protein | Mass: 31198.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: P56965, dimethylargininase |
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#2: Chemical | ChemComp-CIR / |
#3: Chemical | ChemComp-CIT / |
#4: Water | ChemComp-HOH / |
Compound details | INVOLVED IN NITRIC OXIDE GENERATION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.2 % |
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Crystal grow | pH: 5 Details: 100 MM CITRIC ACID/NAOH, 20-40% PEG 8000, 2 MM TCEP, PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000087 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 25, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000087 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. obs: 91675 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.98 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.16→1.2 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 77.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H70 Resolution: 1.2→20 Å / Num. parameters: 24342 / Num. restraintsaints: 30825 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 33 / Occupancy sum hydrogen: 2084.3 / Occupancy sum non hydrogen: 2526.15 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→20 Å
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Refine LS restraints |
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