+Open data
-Basic information
Entry | Database: PDB / ID: 1m4l | ||||||
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Title | STRUCTURE OF NATIVE CARBOXYPEPTIDASE A AT 1.25 RESOLUTION | ||||||
Components | CARBOXYPEPTIDASE A | ||||||
Keywords | HYDROLASE / CARBOXYPEPTIDASE A / METALLOPROTEINASE / METALLOEXOPROTEINASE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Kilshtain-Vardi, A. / Glick, M. / Greenblatt, H.M. / Goldblum, A. / Shoham, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Refined structure of bovine carboxypeptidase A at 1.25 A resolution. Authors: Kilshtain-Vardi, A. / Glick, M. / Greenblatt, H.M. / Goldblum, A. / Shoham, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m4l.cif.gz | 152.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m4l.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 1m4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m4l_validation.pdf.gz | 412.7 KB | Display | wwPDB validaton report |
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Full document | 1m4l_full_validation.pdf.gz | 419 KB | Display | |
Data in XML | 1m4l_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 1m4l_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/1m4l ftp://data.pdbj.org/pub/pdb/validation_reports/m4/1m4l | HTTPS FTP |
-Related structure data
Related structure data | 1ymeS 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: 34445.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A |
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#2: Chemical | ChemComp-ZN / |
#3: 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: 1.82 Å3/Da / Density % sol: 32.4 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 5 ℃ / pH: 7.5 / Method: microdialysisDetails: Shoham, G., (1988) Proc.Natl.Acad.Sci.USA., 85, 684. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.085 / Wavelength: 1.085 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.085 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→30 Å / Num. all: 64976 / Num. obs: 64976 / % possible obs: 86.3 % / Redundancy: 7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.25→1.27 Å / Rmerge(I) obs: 0.127 / % possible all: 36.3 |
Reflection | *PLUS Lowest resolution: 30 Å |
Reflection shell | *PLUS % possible obs: 36.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTERY 1YME Resolution: 1.25→30 Å / Num. parameters: 25563 / Num. restraintsaints: 31254 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.05.
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Refine analyze | Num. disordered residues: 9 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2764.4 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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