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Yorodumi- PDB-4r1q: Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arab... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r1q | ||||||
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Title | Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase in complex with L-arabitol | ||||||
Components | L-arabinose isomerase | ||||||
Keywords | ISOMERASE / Hexamer / Thermophile / thermostable / AI fold | ||||||
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 Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus HTA426 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å | ||||||
Authors | Choi, J.M. / Lee, Y.J. / Lee, D.W. / Lee, S.H. | ||||||
Citation | Journal: to be published Title: Crystal Structure of Thermophilic L-Arabinose Isomerase with L-Arabitol from Geobacillus kaustophilus Authors: Choi, J.M. / Lee, Y.J. / 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 | 4r1q.cif.gz | 610.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r1q.ent.gz | 502.7 KB | Display | PDB format |
PDBx/mmJSON format | 4r1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r1q_validation.pdf.gz | 485.3 KB | Display | wwPDB validaton report |
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Full document | 4r1q_full_validation.pdf.gz | 506.4 KB | Display | |
Data in XML | 4r1q_validation.xml.gz | 114.4 KB | Display | |
Data in CIF | 4r1q_validation.cif.gz | 164.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/4r1q ftp://data.pdbj.org/pub/pdb/validation_reports/r1/4r1q | HTTPS FTP |
-Related structure data
Related structure data | 4r1pS 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: 56304.891 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus HTA426 (bacteria) Gene: araA, GK1904 / Plasmid: pET28a(+)-GKAI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5KYP7, L-arabinose isomerase #2: Chemical | ChemComp-SST / #3: Chemical | ChemComp-MN / #4: Water | ChemComp-HOH / | Sequence details | THIS RESIDUE IS BASED ON YP_147757 OF GENBANK. | |
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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: 2.77 Å3/Da / Density % sol: 55.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 1.8M Na-K phosphate, 4% acetone, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.000001 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2013 |
Radiation | Monochromator: DCM Si(111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000001 Å / Relative weight: 1 |
Reflection | Resolution: 2.248→50 Å / Num. all: 175982 / Num. obs: 174510 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 29.94 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 20.576 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 5.286 / Num. unique all: 8686 / Rsym value: 0.459 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R1P Resolution: 2.248→49.079 Å / FOM work R set: 0.866 / SU ML: 0.23 / σ(F): 1.36 / Phase error: 20.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.44 Å2 / Biso min: 8.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.248→49.079 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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