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Yorodumi- PDB-1zcc: Crystal structure of glycerophosphodiester phosphodiesterase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zcc | ||||||
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Title | Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens str.C58 | ||||||
Components | glycerophosphodiester phosphodiesterase | ||||||
Keywords | HYDROLASE / NYSGXRC / T2047 / Glycerophosphodiester phosphodiesterase / Agrobacterium tumefaciens str. C58 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Agrobacterium tumefaciens str. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Krishnamurthy, N.R. / Kumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit. Authors: Rao, K.N. / Bonanno, J.B. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zcc.cif.gz | 274.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zcc.ent.gz | 223.1 KB | Display | PDB format |
PDBx/mmJSON format | 1zcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/1zcc ftp://data.pdbj.org/pub/pdb/validation_reports/zc/1zcc | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly within the asymmetric unit is a hexamer formed by dimer of trimers. |
-Components
#1: Protein | Mass: 27360.055 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria) Species: Agrobacterium tumefaciens / Strain: C58 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U887, UniProt: A9CG82*PLUS #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Ammonium sulfate, PEG8K, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.4→50 Å / Num. all: 75568 / Num. obs: 75568 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 25.9 Å2 / Rsym value: 0.104 / Net I/σ(I): 14.7 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.4 % / Num. unique all: 7418 / Rsym value: 0.43 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→45.17 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 626023.61 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The residues listed in remark 470 were modelled as ALA due to the lack of electron density. The residues listed in remark 465 were not modelled due to the lack of electron density.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.2296 Å2 / ksol: 0.335671 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→45.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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