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Yorodumi- PDB-3qc3: Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qc3 | ||||||
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Title | Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from HOMO SAPIENS at 2.20 A resolution | ||||||
Components | D-ribulose-5-phosphate-3-epimerase | ||||||
Keywords | ISOMERASE / TIM BARREL FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information ribulose-phosphate 3-epimerase / D-ribulose-phosphate 3-epimerase activity / Pentose phosphate pathway / pentose-phosphate shunt, non-oxidative branch / pentose-phosphate shunt / carbohydrate metabolic process / protein homodimerization activity / extracellular exosome / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from HOMO SAPIENS at 2.20 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 | 3qc3.cif.gz | 191.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qc3.ent.gz | 157 KB | Display | PDB format |
PDBx/mmJSON format | 3qc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/3qc3 ftp://data.pdbj.org/pub/pdb/validation_reports/qc/3qc3 | 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | CRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE-EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25242.686 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPE, HUSSY-17 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q96AT9, ribulose-phosphate 3-epimerase |
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-Non-polymers , 5 types, 208 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THIS CONSTRUCT (RESIDUES 1-224) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 1-224) 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: 2.48 Å3/Da / Density % sol: 50.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.16M magnesium acetate, 10.0% polyethylene glycol 8000, 20.0% Glycerol, 0.1M sodium cacodylate pH 6.0, NANODROP', 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: 0.91837,0.97944,0.97894 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 3, 2009 / Details: FLAT MIRROR (VERTICAL FOCUSING) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING) Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→29.127 Å / Num. obs: 24823 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.791 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.35 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 2.2→29.127 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 10.753 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.188 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.SOLVENTS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.ZINC (ZN), NICKEL (NI) AND IRON (FE) HAVE BEEN MODELED IN THE PUTATIVE ACTIVE SITE AT PARTIAL OCCUPANCIES BASED ON PEAKS IN AN X-RAY FLUORESCENCE EMISSION SPECTRA AND ANOMALOUS DIFFERENCE FOURIER MAPS CALCULATED FROM DIFFRACTION DATA COLLECTED BELOW AND ABOVE THE K-ABSORPTION EDGES FOR THESE METALS. 6.GLYCEROL (GOL) FROM THE CRYSTALLIZATION SOLUTION HAS BEEN MODELED INTO ELECTRON DENSITY AT THE PUTATIVE ACTIVE AND IT MAY BE A SUBSTRATE MIMIC.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.3 Å2 / Biso mean: 46.987 Å2 / Biso min: 28.76 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.127 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 / Number: 2855 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.257 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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