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Yorodumi- PDB-3mc1: Crystal structure of a predicted phosphatase from Clostridium ace... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mc1 | ||||||
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Title | Crystal structure of a predicted phosphatase from Clostridium acetobutylicum | ||||||
Components | Predicted phosphatase, HAD family | ||||||
Keywords | HYDROLASE / PSI2 / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle ...Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Clostridium acetobutylicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å | ||||||
Authors | Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published / Year: 2010 Title: Crystal structure of a predicted phosphatase from Clostridium acetobutylicum Authors: Eswaramoorthy, S. / 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 | 3mc1.cif.gz | 95.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mc1.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 3mc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mc1_validation.pdf.gz | 450.4 KB | Display | wwPDB validaton report |
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Full document | 3mc1_full_validation.pdf.gz | 457.7 KB | Display | |
Data in XML | 3mc1_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 3mc1_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/3mc1 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/3mc1 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 25915.408 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: BL21(DE3)-Codon+RIL(p) - Stratagene / Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CA_C0418 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97LY2 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350; 0.1M BisTris pH 5.5; 0.2M NaCl and Dimethyl sulfoxide, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 21, 2010 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. all: 32453 / Num. obs: 32453 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2922 / Rsym value: 0.306 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.93→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.93→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→2.05 Å / Rfactor Rfree error: 0.025
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