+Open data
-Basic information
Entry | Database: PDB / ID: 1h8l | ||||||||||||
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Title | Duck Carboxypeptidase D Domain II in complex with GEMSA | ||||||||||||
Components | CARBOXYPEPTIDASE GP180 RESIDUES 503-882 | ||||||||||||
Keywords | CARBOXYPEPTIDASE / HYDROLASE / ZINC-DEPENDENT PROTEASE | ||||||||||||
Function / homology | Function and homology information metallocarboxypeptidase D / peptide metabolic process / metallocarboxypeptidase activity / protein processing / proteolysis / extracellular space / zinc ion binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | LOPHONETTA SPECULARIOIDES (crested duck) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Gomis-Rueth, F.X. / Coll, M. / Aviles, F.X. / Vendrell, J. / Fricker, L.D. | ||||||||||||
Citation | Journal: J. Biol. Chem. / Year: 2001 Title: The crystal structure of the inhibitor-complexed carboxypeptidase D domain II and the modeling of regulatory carboxypeptidases. Authors: Aloy, P. / Companys, V. / Vendrell, J. / Aviles, F.X. / Fricker, L.D. / Coll, M. / Gomis-Ruth, F.X. #1: Journal: Embo J. / Year: 1999 Title: Crystal Structure of Avian Carboxypeptidase D Domain II : A Prototype for the Regulatory Metallocarboxypeptidase Subfamily Authors: Gomis-Rueth, F.X. / Companys, V. / Qian, Y. / Fricker, L.D. / Vendrell, J. / Aviles, F.X. / Coll, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h8l.cif.gz | 99.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h8l.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h8l_validation.pdf.gz | 542 KB | Display | wwPDB validaton report |
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Full document | 1h8l_full_validation.pdf.gz | 550.4 KB | Display | |
Data in XML | 1h8l_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 1h8l_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/1h8l ftp://data.pdbj.org/pub/pdb/validation_reports/h8/1h8l | HTTPS FTP |
-Related structure data
Related structure data | 1qmuS 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 on special symmetry positions |
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Details | BIOLOGICAL_UNIT: MONOMER |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43337.297 Da / Num. of mol.: 1 / Fragment: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) LOPHONETTA SPECULARIOIDES (crested duck) Description: OBTAINED BY OVEREXPRESSION FROM A PICHIA PASTORIS SYSTEM. Organ: LIVER / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM71 / References: UniProt: Q90240, UniProt: P83852*PLUS |
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-Sugars , 3 types, 3 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 196 molecules
#4: Chemical | ChemComp-GEM / ( |
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#6: Chemical | ChemComp-SO4 / |
#7: Chemical | ChemComp-ZN / |
#8: 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: 4.6 Å3/Da / Density % sol: 73 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.2 / Details: pH 5.20 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, sitting drop / Details: Gomis-Rueth, F.X., (1999) Embo J., 18, 5817. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8437 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8437 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→43 Å / Num. obs: 26360 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 43.03 Å / % possible obs: 100 % / Num. measured all: 362074 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QMU Resolution: 2.6→43 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.6→43 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 43.03 Å / Rfactor all: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |