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Yorodumi- PDB-3hwp: Crystal structure and computational analyses provide insights int... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hwp | ||||||
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Title | Crystal structure and computational analyses provide insights into the catalytic mechanism of 2, 4-diacetylphloroglucinol hydrolase PhlG from Pseudomonas fluorescens | ||||||
Components | PhlG | ||||||
Keywords | HYDROLASE / beta-grip fold | ||||||
Function / homology | 2,4-diacetylphloroglucinol hydrolase / DAPG hydrolase, PhiG domain / DAPG hydrolase PhiG domain / hydrolase activity / metal ion binding / NICKEL (II) ION / 2,4-diacetylphloroglucinol hydrolase Function and homology information | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | He, Y.-X. / Huang, L. / Xue, Y. / Fei, X. / Teng, Y.-B. / Zhou, C.-Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal Structure and Computational Analyses Provide Insights into the Catalytic Mechanism of 2,4-Diacetylphloroglucinol Hydrolase PhlG from Pseudomonas fluorescens. Authors: He, Y.X. / Huang, L. / Xue, Y. / Fei, X. / Teng, Y.B. / Rubin-Pitel, S.B. / Zhao, H. / Zhou, C.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hwp.cif.gz | 131.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hwp.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hwp_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
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Full document | 3hwp_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 3hwp_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 3hwp_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/3hwp ftp://data.pdbj.org/pub/pdb/validation_reports/hw/3hwp | 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35484.145 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: Pf-5 / Gene: PhlG / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta (DE3) / References: UniProt: Q4K423 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-NI / | #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: 2.77 Å3/Da / Density % sol: 55.61 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% polyethylene glycol 4,000, 17% isopropanol, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9794, 0.9799, 0.9752 | ||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 5, 2008 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. obs: 53600 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.54 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 18.1 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.3 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→25.991 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.87 / 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 / Bsol: 49.435 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.63 Å2 / Biso mean: 27.544 Å2 / Biso min: 14.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.991 Å
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Refine LS restraints |
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LS refinement shell |
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