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Yorodumi- PDB-3mj4: Crystal structure of UDP-galactopyranose mutase in complex with p... -
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-Basic information
Entry | Database: PDB / ID: 3mj4 | ||||||
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Title | Crystal structure of UDP-galactopyranose mutase in complex with phosphonate analog of UDP-galactopyranose | ||||||
Components | UDP-galactopyranose mutase | ||||||
Keywords | ISOMERASE / UDP-galactopyranose mutase / phosphonate analog / inhibitor / binding mode | ||||||
Function / homology | Function and homology information UDP-galactopyranose mutase activity / flavin adenine dinucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Karunan Partha, S. / Sadeghi-Khomami, A. / Slowski, K. / Kotake, T. / Thomas, N.R. / Jakeman, D.L. / Sanders, D.A.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Chemoenzymatic Synthesis, Inhibition Studies, and X-ray Crystallographic Analysis of the Phosphono Analog of UDP-Galp as an Inhibitor and Mechanistic Probe for UDP-Galactopyranose Mutase. Authors: Partha, S.K. / Sadeghi-Khomami, A. / Slowski, K. / Kotake, T. / Thomas, N.R. / Jakeman, D.L. / Sanders, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mj4.cif.gz | 757.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mj4.ent.gz | 632.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mj4_validation.pdf.gz | 5.7 MB | Display | wwPDB validaton report |
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Full document | 3mj4_full_validation.pdf.gz | 5.9 MB | Display | |
Data in XML | 3mj4_validation.xml.gz | 143.2 KB | Display | |
Data in CIF | 3mj4_validation.cif.gz | 189.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/3mj4 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/3mj4 | HTTPS FTP |
-Related structure data
Related structure data | 3hdqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 12 molecules ABCDEFGHIJ
#1: Protein | Mass: 45741.824 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: R1 / Gene: DR_A0367, DR_AO367 / Plasmid: PEHISTEV / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner / References: UniProt: Q9RYF1, UDP-galactopyranose mutase #6: Sugar | |
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-Non-polymers , 5 types, 658 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-UDP / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-URM / ((( | #7: 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: 2.88 Å3/Da / Density % sol: 57.35 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 6.5 Details: 0.1 M HEPES PH 6.5, 0.2 M LICL, 28% PEG 6000, Microbatch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→102.06 Å / Num. obs: 162540 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3HDQ Resolution: 2.65→44.542 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 28.9 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.251 Å2 / ksol: 0.408 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.65→44.542 Å
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Refine LS restraints |
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LS refinement shell |
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