+Open data
-Basic information
Entry | Database: PDB / ID: 1f57 | ||||||
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Title | CARBOXYPEPTIDASE A COMPLEX WITH D-CYSTEINE AT 1.75 A | ||||||
Components | CARBOXYPEPTIDASE A | ||||||
Keywords | HYDROLASE / metalloprotease inhibitor | ||||||
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: 1.75 Å | ||||||
Authors | van Aalten, D.M. / Chong, C.R. / Joshua-Tor, L. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structure of carboxypeptidase A complexed with D-cysteine at 1.75 A - inhibitor-induced conformational changes. Authors: van Aalten, D.M. / Chong, C.R. / Joshua-Tor, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f57.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f57.ent.gz | 59.1 KB | Display | PDB format |
PDBx/mmJSON format | 1f57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f57_validation.pdf.gz | 380 KB | Display | wwPDB validaton report |
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Full document | 1f57_full_validation.pdf.gz | 381.5 KB | Display | |
Data in XML | 1f57_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | 1f57_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/1f57 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/1f57 | HTTPS FTP |
-Related structure data
Related structure data | 5cpaS 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) / References: UniProt: P00730, carboxypeptidase A |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-DCY / |
#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: 2.12 Å3/Da / Density % sol: 41.95 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: microdialysis / pH: 6 / Details: LiCl, MES, pH 6.0, MICRODIALYSIS, temperature 18K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→15 Å / Num. all: 99346 / Num. obs: 28954 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2679 / % possible all: 92.9 |
Reflection | *PLUS Num. measured all: 99346 |
Reflection shell | *PLUS % possible obs: 92.9 % / Num. unique obs: 2679 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CPA excluding Zn and waters Resolution: 1.75→14.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 310380.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46 Å2 / ksol: 0.309 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→14.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.5 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.229 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.188 |