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Yorodumi- PDB-6wk0: Crystal structure of human ribokinase in complex with AMPPCP and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wk0 | ||||||
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Title | Crystal structure of human ribokinase in complex with AMPPCP and ribose | ||||||
Components | Ribokinase | ||||||
Keywords | TRANSFERASE / Enzyme-substrate complex | ||||||
Function / homology | Function and homology information ribokinase / ribokinase activity / Pentose phosphate pathway / D-ribose catabolic process / pentose-phosphate shunt / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Park, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structures of human ribokinase Authors: Park, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wk0.cif.gz | 503 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wk0.ent.gz | 412.8 KB | Display | PDB format |
PDBx/mmJSON format | 6wk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wk0 ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wk0 | HTTPS FTP |
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-Related structure data
Related structure data | 6wjzC 5c41S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 33740.398 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBKS, RBSK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H477, ribokinase #2: Chemical | ChemComp-ACP / #3: Chemical | ChemComp-NA / #4: Sugar | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.36 Å3/Da / Density % sol: 47.85 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, 8% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→51.43 Å / Num. obs: 87255 / % possible obs: 98.64 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.45 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.059 / Rrim(I) all: 0.113 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.36 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4039 / CC1/2: 0.485 / Rpim(I) all: 0.541 / Rrim(I) all: 1.019 / % possible all: 93.15 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5C41 Resolution: 2→51.43 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.447 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 38.676 Å2
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Refinement step | Cycle: 1 / Resolution: 2→51.43 Å
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Refine LS restraints |
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