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Yorodumi- PDB-2hcf: Crystal structure of hydrolase haloacid dehalogenase-like family ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hcf | ||||||
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Title | Crystal structure of hydrolase haloacid dehalogenase-like family (np_662590.1) from Chlorobium tepidum TLS at 1.80 A resolution | ||||||
Components | Hydrolase, haloacid dehalogenase-like family | ||||||
Keywords | HYDROLASE / np_662590.1 / hydrolase haloacid dehalogenase-like family / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chlorobaculum tepidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of hydrolase haloacid dehalogenase-like family (np_662590.1) from Chlorobium tepidum TLS at 1.80 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hcf.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hcf.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 2hcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hcf_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 2hcf_full_validation.pdf.gz | 426.2 KB | Display | |
Data in XML | 2hcf_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 2hcf_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/2hcf ftp://data.pdbj.org/pub/pdb/validation_reports/hc/2hcf | HTTPS FTP |
-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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-Components
#1: Protein | Mass: 26194.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobaculum tepidum (bacteria) / Gene: np_662590.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KBS5 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.01 Å3/Da / Density % sol: 38.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5 Details: 0.2M MgCl2, 30.0% PEG-4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97915, 0.97929 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 5, 2006 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→27.951 Å / Num. obs: 21098 / % possible obs: 92.2 % / Biso Wilson estimate: 25.562 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→27.951 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.882 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.144 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. MG MODELED IN THE ACTIVE SITE BASED ON CRYSTALLIZATION CONDITIONS AND RELATED STRUCTURES. 4. MG MODELED NEAR GLU 63 BASED ON GEOMETRY AND CRYSTLLIZATION CONDITIONS. 5. CHLORINE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 6. RESIDUES 40-42 WERE DISORDERED AND NOT MODELED. 7. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.764 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→27.951 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 22.239 Å / Origin y: 44.9764 Å / Origin z: 15.7082 Å
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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