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Yorodumi- PDB-3bf5: Crystal structure of putative ribokinase (10640157) from Thermopl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bf5 | ||||||
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Title | Crystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91 A resolution | ||||||
Components | Ribokinase related protein | ||||||
Keywords | TRANSFERASE / 10640157 / putative ribokinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information inosine metabolic process / guanosine metabolic process / cytidine kinase / nucleoside kinase activity / inosine kinase / inosine kinase activity / guanosine binding / cytidine metabolic process / adenosine kinase / adenosine kinase activity ...inosine metabolic process / guanosine metabolic process / cytidine kinase / nucleoside kinase activity / inosine kinase / inosine kinase activity / guanosine binding / cytidine metabolic process / adenosine kinase / adenosine kinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / nucleoside phosphate biosynthetic process / adenosine metabolic process / cytidine kinase activity / phosphorylation / GTP binding / ATP binding Similarity search - Function | ||||||
Biological species | Thermoplasma acidophilum DSM 1728 (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.91 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of putative ribokinase (10640157) from Thermoplasma acidophilum at 1.91 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 CONSTRUCT ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE CONSTRUCT WAS ENGINEERED WITH THE FOLLOWING MUTATIONS: E112A, K113A, K115A. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bf5.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bf5.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bf5_validation.pdf.gz | 473.9 KB | Display | wwPDB validaton report |
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Full document | 3bf5_full_validation.pdf.gz | 486.2 KB | Display | |
Data in XML | 3bf5_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 3bf5_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/3bf5 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/3bf5 | HTTPS FTP |
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: MSE / Refine code: 5 / Auth seq-ID: 1 - 282 / Label seq-ID: 20 - 301
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-Components
#1: Protein | Mass: 35647.117 Da / Num. of mol.: 2 / Mutation: E112A, K113A, K115A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic) Species: Thermoplasma acidophilum / Strain: DSM 1728, AMRC-C165, IFO 15155, JCM 9062 / Gene: 10640157, Ta0880 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9HJT3 #2: Chemical | ChemComp-PGO / #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | Sequence details | REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: 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: 2.08 Å3/Da / Density % sol: 40.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: NANODROP, 40.0% 1,2-propanediol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97939, 0.97953 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.91→29.185 Å / Num. obs: 46740 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.803 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.78 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.91→29.185 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.13 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.155 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. 1,2-PROPANEDIOL (PGO) IS MODELED FROM THE CRYSTALLIZATION CONDITION.
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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: 34.325 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→29.185 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.91→1.96 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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