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Yorodumi- PDB-4hwg: Structure of UDP-N-acetylglucosamine 2-epimerase from Rickettsia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hwg | ||||||
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Title | Structure of UDP-N-acetylglucosamine 2-epimerase from Rickettsia bellii | ||||||
Components | UDP-N-acetylglucosamine 2-epimerase | ||||||
Keywords | ISOMERASE / SSGCID / UDP-N-acetylglucosamine 2-epimerase / epimerase / UDP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase activity Similarity search - Function | ||||||
Biological species | Rickettsia bellii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of UDP-N-acetylglucosamine 2-epimerase from Rickettsia bellii Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Sankaran, B. / Davies, D.R. / Edwards, T.E. / Staker, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hwg.cif.gz | 164.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hwg.ent.gz | 128.4 KB | Display | PDB format |
PDBx/mmJSON format | 4hwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hwg_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 4hwg_full_validation.pdf.gz | 440.2 KB | Display | |
Data in XML | 4hwg_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 4hwg_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/4hwg ftp://data.pdbj.org/pub/pdb/validation_reports/hw/4hwg | HTTPS FTP |
-Related structure data
Related structure data | 3beoS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44420.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rickettsia bellii (bacteria) / Strain: RML369-C / Gene: RBE_0708, rffE / Plasmid: RibeA.00061.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q1RIM5, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-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: 50.5 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Emerald Bio JCSG+ D5: 1.6M Na/K phosphate, 100mM HEPES pH 7.5, RibeA.00061.a.B1.PW36203 29.7mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→50 Å / Num. all: 29717 / Num. obs: 29671 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 30.303 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.75 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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 3beo, modified with ccp4 program CHAINSAW Resolution: 2→43.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1693 / WRfactor Rwork: 0.1362 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9005 / SU B: 5.729 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1357 / SU Rfree: 0.124 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 85.09 Å2 / Biso mean: 33.1379 Å2 / Biso min: 8.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 15.705 Å / Origin y: 16.675 Å / Origin z: 33.583 Å
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Refinement TLS group |
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