+Open data
-Basic information
Entry | Database: PDB / ID: 5vhu | ||||||
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Title | E. coli CFT073 c3406 | ||||||
Components | Isomerase | ||||||
Keywords | ISOMERASE / Sugar isomerase domain / arabinose-5-phosphate isomerase / API | ||||||
Function / homology | Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Cech, D.L. / Pratt, A.C. / Woodard, R.W. | ||||||
Citation | Journal: To Be Published Title: Insights into the mechanism of arabinose-5-phosphate isomerases. Authors: Cech, D.L. / Pratt, A.C. / Cheng, M. / Barraza, S. / Yep, A. / Holler, T.P. / Woodard, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vhu.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vhu.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vhu_validation.pdf.gz | 419.1 KB | Display | wwPDB validaton report |
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Full document | 5vhu_full_validation.pdf.gz | 419.1 KB | Display | |
Data in XML | 5vhu_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 5vhu_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/5vhu ftp://data.pdbj.org/pub/pdb/validation_reports/vh/5vhu | HTTPS FTP |
-Related structure data
Related structure data | 5uqiC 3fxaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20912.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: OK10_20845 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A148HHT8 |
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#2: Chemical | ChemComp-SO4 / |
#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: 2.37 Å3/Da / Density % sol: 48.12 % / Description: colorless rods |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M sodium citrate tribasic pH 5.6, 0.5 M NaCl, 2% v/v ethylene imine polymer |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→52.6 Å / Num. obs: 17785 / % possible obs: 99.85 % / Redundancy: 14.7 % / Rsym value: 0.072 / Net I/σ(I): 10.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FXA Resolution: 1.8→52.6 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.949 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.111
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.962 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→52.6 Å
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Refine LS restraints |
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