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Yorodumi- PDB-1ghd: Crystal structure of the glutaryl-7-aminocephalosporanic acid acy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ghd | ||||||
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Title | Crystal structure of the glutaryl-7-aminocephalosporanic acid acylase by mad phasing | ||||||
Components | (GLUTARYL-7-AMINOCEPHALOSPORANIC ACID ACYLASE) x 2 | ||||||
Keywords | HYDROLASE / cephalosporin acylase | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. 130 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Ding, Y. / Jiang, W. / Mao, X. / He, H. / Zhang, S. / Tang, H. / Bartlam, M. / Ye, S. / Jiang, F. / Liu, Y. ...Ding, Y. / Jiang, W. / Mao, X. / He, H. / Zhang, S. / Tang, H. / Bartlam, M. / Ye, S. / Jiang, F. / Liu, Y. / Zhao, G. / Rao, Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Affinity alkylation of the Trp-B4 residue of the beta -subunit of the glutaryl 7-aminocephalosporanic acid acylase of Pseudomonas sp. 130. Authors: Huang, X. / Zeng, R. / Ding, X. / Mao, X. / Ding, Y. / Rao, Z. / Xie, Y. / Jiang, W. / Zhao, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ghd.cif.gz | 145.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ghd.ent.gz | 115.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ghd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/1ghd ftp://data.pdbj.org/pub/pdb/validation_reports/gh/1ghd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18737.322 Da / Num. of mol.: 1 / Fragment: ALPHA-SUBUNIT + SPACER PEPTIDE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. 130 (bacteria) / Plasmid: PMFT7H6CAII / Production host: Escherichia coli (E. coli) References: UniProt: O86089, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
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#2: Protein | Mass: 58855.785 Da / Num. of mol.: 1 / Fragment: BETA-SUBUNIT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. 130 (bacteria) / Plasmid: PMFT7H6CAII / Production host: Escherichia coli (E. coli) References: UniProt: O86089, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides |
#3: 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: 3.32 Å3/Da / Density % sol: 62.98 % |
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Crystal grow | Temperature: 291 K / Method: hanging drop/vapor diffusion / pH: 7.5 Details: sodium acetate, cadmium sulfate, hepes, pH 7.5, HANGING DROP/VAPOR DIFFUSION, temperature 291.0K |
Crystal grow | *PLUS Method: unknown / Details: Ichikawa, S., (1981) Agric. Biol. Chem., 45, 2231. |
-Data collection
Diffraction | Mean temperature: 115 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9639 |
Detector | Type: SBC-2 / Detector: CCD / Date: Nov 8, 2000 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9639 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. all: 69082 / Num. obs: 68105 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.48 / Num. unique all: 5097 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Resolution: 2.4→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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