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Yorodumi- PDB-7ys9: Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ys9 | ||||||
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Title | Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) in complex with both UDP-Glucose and UDP-Galactose in chainA from Mycobacterium tuberculosis | ||||||
Components | UDP-glucose 4-epimerase | ||||||
Keywords | ISOMERASE / GalE1 / UDP-glucose 4-epimerase / Rv3634c / UDP-Glucose / UDP-Galactose / Mycobacterium tuberculosis | ||||||
Function / homology | Function and homology information UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose metabolic process / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Yadav, S. / Bhatia, I. / Biswal, B.K. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of UDP-glucose 4-epimerase (Rv3634c) in complex with both UDP-Glucose and UDP-Galactose in chainA from Mycobacterium tuberculosis Authors: Yadav, S. / Bhatia, I. / Biswal, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ys9.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ys9.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 7ys9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ys9_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7ys9_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7ys9_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 7ys9_validation.cif.gz | 53.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/7ys9 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/7ys9 | HTTPS FTP |
-Related structure data
Related structure data | 7ys8S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34453.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: galE1, Rv3634c / Production host: Mycolicibacterium smegmatis (bacteria) / References: UniProt: P9WN67, UDP-glucose 4-epimerase |
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-Non-polymers , 5 types, 906 molecules
#2: Chemical | #3: Chemical | ChemComp-UPG / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.29 Å3/Da / Density % sol: 46.39 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M Sodium acetate trihydrate, 0.1M Tris pH 8.5 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→35 Å / Num. obs: 67055 / % possible obs: 89.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Χ2: 1.902 / Net I/σ(I): 24.4 / Num. measured all: 198448 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.156 / Num. unique obs: 6764 / CC1/2: 0.963 / Rpim(I) all: 0.106 / Rrim(I) all: 0.19 / Χ2: 1.162 / % possible all: 90.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7YS8 Resolution: 1.65→24.62 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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 max: 55.3 Å2 / Biso mean: 19.08 Å2 / Biso min: 8.96 Å2
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Refinement step | Cycle: final / Resolution: 1.65→24.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.692 Å / Rfactor Rfree error: 0
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