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Yorodumi- PDB-2ci5: Crystal structure of Dimethylarginine Dimethylaminohydrolase I in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ci5 | |||||||||
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Title | Crystal structure of Dimethylarginine Dimethylaminohydrolase I in complex with L-homocysteine | |||||||||
Components | NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE 1 | |||||||||
Keywords | HYDROLASE / NOS REGULATION / S-NITROSYLATION / ZINC / NO / MMA / ADMA / ACETYLATION / METAL-BINDING | |||||||||
Function / homology | Function and homology information protein nitrosylation / eNOS activation / dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / amino acid binding ...protein nitrosylation / eNOS activation / dimethylargininase / dimethylargininase activity / citrulline metabolic process / negative regulation of cellular response to hypoxia / arginine metabolic process / regulation of systemic arterial blood pressure / negative regulation of vascular permeability / amino acid binding / arginine catabolic process / nitric oxide biosynthetic process / positive regulation of nitric oxide biosynthetic process / negative regulation of cell population proliferation / zinc ion binding Similarity search - Function | |||||||||
Biological species | BOS TAURUS (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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 | 2ci5.cif.gz | 129.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ci5.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ci5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2ci5 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2ci5 | HTTPS FTP |
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-Related structure data
Related structure data | 2c6zC 2ci1C 2ci3C 2ci4C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99999, 0.00489, -0.0023), Vector: |
-Components
#1: Protein | Mass: 31198.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: P56965, dimethylargininase #2: Chemical | #3: Chemical | ChemComp-CIT / | #4: Water | ChemComp-HOH / | |
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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: 2.16 Å3/Da / Density % sol: 43 % |
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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: 0.9793 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 11, 2003 / Details: DYNAMICALLY BENDABLE MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 48415 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 3.25 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H70 Resolution: 1.79→29.2 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1453876.18 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.7133 Å2 / ksol: 0.348887 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.79→29.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.085 / Total num. of bins used: 6
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Xplor file |
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