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Yorodumi- PDB-1h70: DDAH FROM PSEUDOMONAS AERUGINOSA. C249S MUTANT COMPLEXED WITH CIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h70 | |||||||||
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Title | DDAH FROM PSEUDOMONAS AERUGINOSA. C249S MUTANT COMPLEXED WITH CITRULLINE | |||||||||
Components | NG, NG-DIMETHYLARGININE DIMETHYLAMINOHYDROLASE | |||||||||
Keywords | HYDROLASE / DDAH / NITRIC OXIDE SYNTHASE INHIBITOR | |||||||||
Function / homology | Function and homology information dimethylargininase / dimethylargininase activity / citrulline metabolic process / arginine metabolic process / amino acid binding / positive regulation of nitric oxide biosynthetic process / metal ion binding Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Murray-Rust, J. / Leiper, J. / McAlister, M. / Phelan, J. / Tilley, S. / Santamaria, J. / Vallance, P. / McDonald, N. | |||||||||
Citation | Journal: Nat. Struct. Biol. / Year: 2001 Title: Structural insights into the hydrolysis of cellular nitric oxide synthase inhibitors by dimethylarginine dimethylaminohydrolase. Authors: Murray-Rust, J. / Leiper, J. / McAlister, M. / Phelan, J. / Tilley, S. / Santa Maria, J. / Vallance, P. / McDonald, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h70.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h70.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 1h70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h70_validation.pdf.gz | 382.4 KB | Display | wwPDB validaton report |
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Full document | 1h70_full_validation.pdf.gz | 385 KB | Display | |
Data in XML | 1h70_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1h70_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/1h70 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/1h70 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28637.631 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9I4E3, dimethylargininase | ||
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#2: Chemical | ChemComp-CIR / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | CHAIN A ENGINEEREDSequence details | PHE A 0 CLONING ARTIFACT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: SITTING DROPS; EQUAL QUANTITIES OF PROTEIN SOLUTION AND WELL SOLUTION. PROTEIN SOLUTION 14 MG/ML IN 50MM TRIS PH8, 5MMDTT, 10:1 MOLAR RATIO OF CITRULLINE. WEEL SOLUTION ).1M TRIS PH 8.5, 0. ...Details: SITTING DROPS; EQUAL QUANTITIES OF PROTEIN SOLUTION AND WELL SOLUTION. PROTEIN SOLUTION 14 MG/ML IN 50MM TRIS PH8, 5MMDTT, 10:1 MOLAR RATIO OF CITRULLINE. WEEL SOLUTION ).1M TRIS PH 8.5, 0.2M NA ACETATE, 25%W/V PEG4000. | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX14.1 / Wavelength: 1.244 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2000 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.244 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→54.2 Å / Num. obs: 20847 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 8 / % possible all: 99 |
Reflection | *PLUS % possible obs: 99.3 % |
Reflection shell | *PLUS % possible obs: 99.8 % / Mean I/σ(I) obs: 8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NATIVE DDAH Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.07 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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