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Yorodumi- PDB-3ct8: Crystal structure of a putative glyoxalase (NP_243026.1) from Bac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ct8 | ||||||
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Title | Crystal structure of a putative glyoxalase (NP_243026.1) from Bacillus halodurans at 2.10 A resolution | ||||||
Components | Putative glyoxalase | ||||||
Keywords | LYASE / NP_243026.1 / Putative Glyoxalase / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus halodurans C-125 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a Putative Glyoxalase (NP_243026.1) from Bacillus halodurans at 2.10 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ct8.cif.gz | 40.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ct8.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ct8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ct8_validation.pdf.gz | 434.6 KB | Display | wwPDB validaton report |
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Full document | 3ct8_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | 3ct8_validation.xml.gz | 8 KB | Display | |
Data in CIF | 3ct8_validation.cif.gz | 9.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ct/3ct8 ftp://data.pdbj.org/pub/pdb/validation_reports/ct/3ct8 | 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 on special symmetry positions |
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 17383.111 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125 / DSM 18197 / FERM 7344 / JCM 9153 / Gene: NP_243026.1, BH2160 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9KAX6 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-UNL / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Water | ChemComp-HOH / |
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: NANODROP, 40.0% MPD, 5.0% PEG 8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.92522, 0.97922, 0.97464 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2008 / Details: Flat mirror (vertical focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.09→26.528 Å / Num. obs: 9659 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 44.118 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 2.1→26.528 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.946 / SU B: 12.209 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.187 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. X-RAY FLUORESCENCE EXCITATION, WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF ZN ION. 5. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED NEAR THE ZN ION SITE.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.793 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→26.528 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.16 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.841 Å / Origin y: 19.915 Å / Origin z: 22.591 Å
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