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Yorodumi- PDB-2apr: STRUCTURE AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION OF THE ASPAR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2apr | |||||||||
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Title | STRUCTURE AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION OF THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS | |||||||||
Components | RHIZOPUSPEPSIN | |||||||||
Keywords | HYDROLASE (ASPARTIC PROTEINASE) | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Rhizopus microsporus var. chinensis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | |||||||||
Authors | Suguna, K. / Davies, D.R. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1987 Title: Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis. Authors: Suguna, K. / Bott, R.R. / Padlan, E.A. / Subramanian, E. / Sheriff, S. / Cohen, G.H. / Davies, D.R. #1: Journal: Biochemistry / Year: 1982 Title: Three-Dimensional Structure of the Complex of the Rhizopus Chinensis Carboxyl Proteinase and Pepstatin at 2.5 Angstroms Resolution Authors: Bott, R.R. / Subramanian, E. / Davies, D.R. #2: Journal: Adv.Exp.Med.Biol. / Year: 1977 Title: The Crystal Structure of an Acid Protease from Rhizopus Chinensis at 2.5 Angstroms Resolution Authors: Subramanian, E. / Liu, M. / Swan, I.D.A. / Davies, D.R. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977 Title: Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica Authors: Subramanian, E. / Swan, I.D.A. / Liu, M. / Davies, D.R. / Jenkins, J.A. / Tickle, I.J. / Blundell, T.L. | |||||||||
History |
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Remark 700 | SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS ...SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *S2A* AND *S2B* REPRESENT ONE BIFURCATED SHEET. SHEETS *S3A* AND *S3B* REPRESENT ONE BIFURCATED SHEET. SHEETS *S4A* AND *S4B* REPRESENT ONE BIFURCATED SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2apr.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2apr.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 2apr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2apr_validation.pdf.gz | 405.5 KB | Display | wwPDB validaton report |
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Full document | 2apr_full_validation.pdf.gz | 407.8 KB | Display | |
Data in XML | 2apr_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2apr_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/2apr ftp://data.pdbj.org/pub/pdb/validation_reports/ap/2apr | 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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Atom site foot note | 1: RESIDUES 26 AND 316 ARE CIS PROLINES. |
-Components
#1: Protein | Mass: 34068.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizopus microsporus var. chinensis (fungus) Species: Rhizopus microsporus / Strain: var. chinensis / References: UniProt: P06026, EC: 3.4.23.6 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.11 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: other | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 38090 / Num. measured all: 129693 / Rmerge(I) obs: 0.043 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Highest resolution: 1.8 Å Details: THERE IS DISORDER AT SER 116, ARG 151, ARG 192, SER 211.
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Refine analyze | Luzzati coordinate error obs: 0.16 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.8 Å
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Refine LS restraints |
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Refinement | *PLUS σ(F): 3 / Highest resolution: 1.8 Å / Num. reflection obs: 31917 / Rfactor obs: 0.143 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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