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Yorodumi- PDB-3pte: THE REFINED CRYSTALLOGRAPHIC STRUCTURE OF A DD-PEPTIDASE PENICILL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pte | |||||||||
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Title | THE REFINED CRYSTALLOGRAPHIC STRUCTURE OF A DD-PEPTIDASE PENICILLIN-TARGET ENZYME AT 1.6 A RESOLUTION | |||||||||
Components | D-ALANYL-D-ALANINE CARBOXYPEPTIDASE TRANSPEPTIDASE | |||||||||
Keywords | HYDROLASE / TRANSPEPTIDASE | |||||||||
Function / homology | Function and homology information serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | Streptomyces sp. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | |||||||||
Authors | Kelly, J.A. / Kuzin, A.P. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 A resolution. Authors: Kelly, J.A. / Kuzin, A.P. #1: Journal: J.Mol.Biol. / Year: 1989 Title: Crystallographic Mapping of Beta-Lactams Bound to a D-Alanyl-D-Alanine Peptidase Target Enzyme Authors: Kelly, J.A. / Knox, J.R. / Zhao, H. / Frere, J.M. / Ghuysen, J.M. #2: Journal: Science / Year: 1986 Title: On the Origin of Bacterial Resistance to Penicillins. Comparison of a Beta-Lactamase, a Penicillin Target Authors: Kelly, J.A. / Dideberg, O. / Charlier, P. / Wery, J.P. / Libert, M. / Moews, P.C. / Knox, J.R. / Duez, C. / Fraipont, Cl. / Joris, B. / Dusart, J. / Frere, J.F. / Ghuysen, J.M. #3: Journal: J.Biol.Chem. / Year: 1985 Title: 2.8 Angstroms Structure of a Penicillin-Sensitive D-Alanyl Carboxypeptidase-Transpeptidase from Streptomyces R61, Complexes with Beta-Lactams Authors: Kelly, J.A. / Knox, J.R. / Moews, P.C. / Hite, G.J. / Bartolone, J.B. / Zhao, H. / Joris, B. / Frere, J.M. / Ghuysen, J.M. | |||||||||
History |
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Remark 650 | HELIX H7 (RESIDUES 235 - 237) AND RESIDUES 61 AND 62 OF H2 ARE 3/10 HELIX. | |||||||||
Remark 700 | SHEET AP1 IN *SHEET* RECORDS BELOW IS A MAJOR ANTIPARALLEL SHEET. AP2 IS A SHORT ANTIPARALLEL SHEET. ...SHEET AP1 IN *SHEET* RECORDS BELOW IS A MAJOR ANTIPARALLEL SHEET. AP2 IS A SHORT ANTIPARALLEL SHEET. M1 IS A SHORT MIXED SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pte.cif.gz | 80.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pte.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 3pte.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pte_validation.pdf.gz | 369.9 KB | Display | wwPDB validaton report |
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Full document | 3pte_full_validation.pdf.gz | 375.3 KB | Display | |
Data in XML | 3pte_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 3pte_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/3pte ftp://data.pdbj.org/pub/pdb/validation_reports/pt/3pte | 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: CIS PROLINE - PRO 201 |
-Components
#1: Protein | Mass: 37422.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: R61 References: UniProt: P15555, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Water | ChemComp-HOH / |
Compound details | THE ACTIVE SITE CONSISTS OF EIGHT RESIDUES IN THREE GROUPS. THREE SHORT SEQUENCE SEGMENTS ARE FOUND ...THE ACTIVE SITE CONSISTS OF EIGHT RESIDUES IN THREE GROUPS. THREE SHORT SEQUENCE SEGMENTS ARE FOUND IN ALL PENICILLIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.69 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | Num. obs: 41176 / % possible obs: 88 % / Observed criterion σ(I): 0 |
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Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.158 |
-Processing
Software |
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Refinement | Resolution: 1.6→20 Å / σ(F): 2
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Displacement parameters | Biso mean: 9.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS
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