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Yorodumi- PDB-3ujh: Crystal structure of substrate-bound Glucose-6-phosphate isomeras... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ujh | ||||||
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Title | Crystal structure of substrate-bound Glucose-6-phosphate isomerase from Toxoplasma gondii | ||||||
Components | Glucose-6-phosphate isomerase | ||||||
Keywords | ISOMERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Toxoplasma gondii (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of substrate-bound Glucose-6-phosphate isomerase from Toxoplasma gondii Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Gardberg, A. / Davies, D. / Staker, B. / Stewart, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ujh.cif.gz | 444.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ujh.ent.gz | 363.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ujh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/3ujh ftp://data.pdbj.org/pub/pdb/validation_reports/uj/3ujh | HTTPS FTP |
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-Related structure data
Related structure data | 3pr3S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 63558.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGME49_083780 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B6KMQ4, glucose-6-phosphate isomerase #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 47.8 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Internal tracking number 226935D6. The crystallant was JCSG screen condition D6: 30% PEG 8000, 0.1 M Tris 8.5, 200 mM MgCl2. The protein solution was TogoA.17127.a.A1 PW28176 at 26.2 mg/mL ...Details: Internal tracking number 226935D6. The crystallant was JCSG screen condition D6: 30% PEG 8000, 0.1 M Tris 8.5, 200 mM MgCl2. The protein solution was TogoA.17127.a.A1 PW28176 at 26.2 mg/mL in a stabilizing buffer of 500 mM NaCl, 25 mM HEPES, 5% glycerol, 0.025% azide, 2 mM DTT, pH 7.0 with 10mM Glucose-6-phosphate. 0.4 + 0.4 uL sitting drop vapor diffusion. Cryoprotection: 20% ethylene glycol., vapor diffusion, sitting drop, temperature 290K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 28, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 67619 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 22.775 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 8.86 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3PR3 Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.241 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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: 16.471 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 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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