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Yorodumi- PDB-3qqw: Crystal structure of a putative lyase (Reut_B4148) from Ralstonia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qqw | ||||||
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Title | Crystal structure of a putative lyase (Reut_B4148) from Ralstonia eutropha JMP134 at 2.44 A resolution | ||||||
Components | Putative citrate lyaseATP citrate synthase | ||||||
Keywords | LYASE / TIM BETA/ALPHA-BARREL / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ralstonia eutropha (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.44 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a Hypothetical lyase (Reut_B4148) from Ralstonia eutropha JMP134 at 2.44 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 | 3qqw.cif.gz | 655.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qqw.ent.gz | 564 KB | Display | PDB format |
PDBx/mmJSON format | 3qqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/3qqw ftp://data.pdbj.org/pub/pdb/validation_reports/qq/3qqw | 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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Unit cell |
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Details | CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A TRIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. |
-Components
#1: Protein | Mass: 36542.934 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: JMP134 / LMG 1197 / Gene: Reut_B4148 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46TN2 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.32 Å3/Da / Density % sol: 47.01 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R MERGE, COMPLETENESS AND Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.93 | Details: 1.00M lithium chloride, 20.100% polyethylene glycol 6000, 0.1M MES pH 5.93, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97916 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97916 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.44→29.793 Å / Num. obs: 74753 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 51.127 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.15 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.44→29.793 Å / Cor.coef. Fo:Fc: 0.9343 / Cor.coef. Fo:Fc free: 0.9198 / Occupancy max: 1 / Occupancy min: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. CHLORIDE (CL) FROM THE CRYSTALLIZATION CONDITION HAS BEEN MODELED IN THE SOLVENT STRUCTURE. 4. NCS RESTRAINTS WERE APPLIED USING BUSTERS LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE REFINEMENT WAS RESTRAINED AGAINST THE SAD PHASES.
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Displacement parameters | Biso max: 159.5 Å2 / Biso mean: 57.5643 Å2 / Biso min: 10.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.44→29.793 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.44→2.5 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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