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Yorodumi- PDB-1dtd: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE LEECH CARBOXYPEPTIDA... -
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-Basic information
Entry | Database: PDB / ID: 1dtd | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE LEECH CARBOXYPEPTIDASE INHIBITOR AND THE HUMAN CARBOXYPEPTIDASE A2 (LCI-CPA2) | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Carboxypeptidase A2 / Leech Carboxypeptidase Inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information carboxypeptidase A2 / protein catabolic process in the vacuole / peptidase inhibitor activity / vacuole / metallocarboxypeptidase activity / carboxypeptidase activity / proteolysis / extracellular space / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.65 Å | ||||||
Authors | Reverter, D. / Fernandez-Catalan, C. / Bode, W. / Holak, T.A. / Aviles, F.X. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Structure of a novel leech carboxypeptidase inhibitor determined free in solution and in complex with human carboxypeptidase A2. Authors: Reverter, D. / Fernandez-Catalan, C. / Baumgartner, R. / Pfander, R. / Huber, R. / Bode, W. / Vendrell, J. / Holak, T.A. / Aviles, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dtd.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dtd.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dtd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dtd_validation.pdf.gz | 394.9 KB | Display | wwPDB validaton report |
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Full document | 1dtd_full_validation.pdf.gz | 402.5 KB | Display | |
Data in XML | 1dtd_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1dtd_validation.cif.gz | 16.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dtd ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dtd | HTTPS FTP |
-Related 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: 33660.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48052, peptidyl-dipeptidase A |
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#2: Protein | Mass: 6787.647 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hirudo medicinalis (medicinal leech) / References: UniProt: P81511 |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-GLU / |
#5: 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: 2.64 Å3/Da / Density % sol: 53.43 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: ammonium phosphate, sodium citrate, pH 7.5, VAPOR DIFFUSION, temperature 298.0K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4, 20 ℃ / Method: vapor diffusion, sitting dropDetails: drop consists of equal volume of protein and reservoir solutions PH range low: 8.5 / PH range high: 6 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 433570 / Num. obs: 52605 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5 / Redundancy: 5 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 80 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 6 % / Rmerge(I) obs: 0.15 / Num. unique all: 3567 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 433570 |
Reflection shell | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Resolution: 1.65→12 Å / σ(F): 2 / σ(I): 5
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Refinement step | Cycle: LAST / Resolution: 1.65→12 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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