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Yorodumi- PDB-4q7q: The crystal structure of a possible lipase from Chitinophaga pine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q7q | ||||||
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Title | The crystal structure of a possible lipase from Chitinophaga pinensis DSM 2588 | ||||||
Components | Lipolytic protein G-D-S-L familyLipolysis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / protein structure initiative / MCSG / Midwest Center for Structural Genomics | ||||||
Function / homology | SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / Lipolytic protein G-D-S-L family Function and homology information | ||||||
Biological species | Chitinophaga pinensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.451 Å | ||||||
Authors | Tan, K. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a possible lipase from Chitinophaga pinensis DSM 2588 Authors: Tan, K. / Tesar, C. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q7q.cif.gz | 229.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q7q.ent.gz | 194 KB | Display | PDB format |
PDBx/mmJSON format | 4q7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/4q7q ftp://data.pdbj.org/pub/pdb/validation_reports/q7/4q7q | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30013.492 Da / Num. of mol.: 2 / Fragment: UNP residues 20-282 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chitinophaga pinensis (bacteria) / Strain: DSM 2588 / Gene: Cpin_6674 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: C7PNH7 #2: Chemical | ChemComp-PG4 / | #3: Chemical | #4: Chemical | ChemComp-FMT / #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: 2.52 Å3/Da / Density % sol: 51.13 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 0.1M CHES:NaOH, 30% (v/v) PEG 400, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2014 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→30.2 Å / Num. all: 104383 / Num. obs: 104383 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 9.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 46.3 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5192 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.451→30.2 Å / SU ML: 0.14 / σ(F): 1.39 / Phase error: 17.05 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.451→30.2 Å
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Refine LS restraints |
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LS refinement shell |
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