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Yorodumi- PDB-4q0q: Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q0q | ||||||
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Title | Crystal structure of Acinetobacter sp. DL28 L-ribose isomerase in complex with L-ribulose | ||||||
Components | L-Ribose isomerase | ||||||
Keywords | ISOMERASE / Cupin barrel / Sugar binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Acinetobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Yoshida, H. / Yoshihara, A. / Teraoka, M. / Izumori, K. / Kamitori, S. | ||||||
Citation | Journal: Febs J. / Year: 2014 Title: X-ray structure of a novel L-ribose isomerase acting on a non-natural sugar L-ribose as its ideal substrate. Authors: Yoshida, H. / Yoshihara, A. / Teraoka, M. / Terami, Y. / Takata, G. / Izumori, K. / Kamitori, S. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Overexpression, crystallization and preliminary X-ray diffraction analysis of L-ribose isomerase from Acinetobacter sp. strain DL-28 Authors: Yoshida, H. / Teraoka, M. / Yoshihara, A. / Izumori, K. / Kamitori, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q0q.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q0q.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 4q0q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/4q0q ftp://data.pdbj.org/pub/pdb/validation_reports/q0/4q0q | HTTPS FTP |
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-Related structure data
Related structure data | 4q0pSC 4q0sC 4q0uC 4q0vC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28751.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter (bacteria) / Strain: DL-28 / Gene: L-RI / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q93UQ5, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds |
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-Sugars , 2 types, 8 molecules
#3: Sugar | ChemComp-RUU / #4: Sugar | ChemComp-QDK / | |
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-Non-polymers , 3 types, 93 molecules
#2: Chemical | ChemComp-CO / |
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#5: Chemical | ChemComp-NCO / |
#6: 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: 2.63 Å3/Da / Density % sol: 53.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10-16%(v/v) PEG400, 0.2M NaCl, 0.1M HEPES, 0.02M Hexaammine cobalt(III) chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jan 14, 2012 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→20.5 Å / Num. all: 22933 / Num. obs: 22933 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.93→2 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2287 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4Q0P Resolution: 1.93→20.45 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 7042759.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.6214 Å2 / ksol: 0.5 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.93→20.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→2 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
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Xplor file |
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