[English] 日本語
Yorodumi- PDB-2ci4: Crystal Structure of Dimethylarginine dimethylaminohydrolase I cr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ci4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Dimethylarginine dimethylaminohydrolase I crystal form II | ||||||
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 / 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: 1.7 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 Inhibitors. Authors: Frey, D. / Braun, O. / Briand, C. / Vasak, M. / Grutter, M.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ci4.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ci4.ent.gz | 50.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ci4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ci4_validation.pdf.gz | 422.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ci4_full_validation.pdf.gz | 428.1 KB | Display | |
Data in XML | 2ci4_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 2ci4_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2ci4 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2ci4 | HTTPS FTP |
-Related structure data
Related structure data | 2c6zC 2ci1C 2ci3C 2ci5C 2ci6C 2ci7C 1h70S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.74 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9793 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 11, 2003 |
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: 1.7→30 Å / Num. obs: 32693 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.45 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.8 / % possible all: 93.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H70 Resolution: 1.7→29.77 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 888688.99 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: CNS BULK SOLVENT MODEL USED / Bsol: 41.2417 Å2 / ksol: 0.358626 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.71 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→29.77 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|