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Yorodumi- PDB-2rfh: Crystal Structure Analysis of CPA-2-benzyl-3-nitropropanoic acid ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rfh | ||||||
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Title | Crystal Structure Analysis of CPA-2-benzyl-3-nitropropanoic acid complex | ||||||
Components | Carboxypeptidase A1 | ||||||
Keywords | HYDROLASE / protein-inhibitor complex / Carboxypeptidase | ||||||
Function / homology | Function and homology information carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Wang, S.-F. / Zeng, Z.-H. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2008 Title: Nitro as a novel zinc-binding group in the inhibition of carboxypeptidase A Authors: Wang, S.-H. / Wang, S.-F. / Xuan, W. / Zeng, Z.-H. / Jin, J.-Y. / Ma, J. / Tian, G.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rfh.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rfh.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 2rfh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rfh_validation.pdf.gz | 444.7 KB | Display | wwPDB validaton report |
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Full document | 2rfh_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 2rfh_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2rfh_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/2rfh ftp://data.pdbj.org/pub/pdb/validation_reports/rf/2rfh | 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
#1: Protein | Mass: 34445.418 Da / Num. of mol.: 1 / Fragment: ligand binding domain / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Pancreas References: UniProt: A6H6Y4, UniProt: P00730*PLUS, carboxypeptidase A |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-23N / ( |
#4: Water | ChemComp-HOH / |
-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: 34.27 % |
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Crystal grow | Temperature: 277 K / Method: soaking / pH: 7.5 / Details: LiCl, Tris, pH 7.5, soaking, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 16, 2007 / Details: confocal | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→38.42 Å / Num. obs: 27657 / % possible obs: 98.7 % / Redundancy: 7.16 % / Rmerge(I) obs: 0.045 / Χ2: 0.8 / Net I/σ(I): 30.2 / Scaling rejects: 2242 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 2.279 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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