+Open data
-Basic information
Entry | Database: PDB / ID: 7cxo | ||||||
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Title | Crystal structure of Arabinose isomerase from hybrid AI10 | ||||||
Components | L-arabinose isomerase | ||||||
Keywords | ISOMERASE / hybrid / Arabinose isomerase | ||||||
Function / homology | Function and homology information L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to xylulose 5-phosphate / manganese ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Alicyclobacillus sp. TP-7 (bacteria) Geobacillus kaustophilus (bacteria) Escherichia coli O157:H7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Hoang, N.K.Q. / Dhanasingh, I. / Cao, T.P. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Arabinose isomerase from hyper thermophilic hybrid AI10 Authors: Hoang, N.K.Q. / Dhanasingh, I. / Cao, T.P. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cxo.cif.gz | 573.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cxo.ent.gz | 473.9 KB | Display | PDB format |
PDBx/mmJSON format | 7cxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cxo_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7cxo_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7cxo_validation.xml.gz | 102.1 KB | Display | |
Data in CIF | 7cxo_validation.cif.gz | 137.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/7cxo ftp://data.pdbj.org/pub/pdb/validation_reports/cx/7cxo | HTTPS FTP |
-Related structure data
Related structure data | 2ajtS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 55918.539 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: Chimeric protein Source: (gene. exp.) Alicyclobacillus sp. TP-7 (bacteria), (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria), (gene. exp.) Escherichia coli O157:H7 (bacteria) Gene: araA, araA, GK1904, araA, Z0070, ECs0066 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: K0IGW6, UniProt: Q5KYP7, UniProt: P58538, L-arabinose isomerase #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MN / #4: Water | ChemComp-HOH / | 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: 2.37 Å3/Da / Density % sol: 48.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 30% (v/v) Polyethylene glycol 400, 100mM Sodium cacodylate/ Hydrochloric acid pH 6.5, 200mM Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.2→50 Å / Num. obs: 54358 / % possible obs: 99.8 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.062 / Rrim(I) all: 0.197 / Χ2: 0.643 / Net I/σ(I): 3.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AJT Resolution: 3.2→48.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.882 / SU B: 29.624 / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 204.28 Å2 / Biso mean: 75.389 Å2 / Biso min: 17.43 Å2
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Refinement step | Cycle: final / Resolution: 3.2→48.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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