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Yorodumi- PDB-4r1p: Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arab... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r1p | ||||||
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Title | Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase with Mn2+ | ||||||
Components | L-arabinose isomerase | ||||||
Keywords | ISOMERASE / Hexamer / Themophile / 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: 2.297 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 with Mn2+ 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 | 4r1p.cif.gz | 596.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r1p.ent.gz | 492.7 KB | Display | PDB format |
PDBx/mmJSON format | 4r1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/4r1p ftp://data.pdbj.org/pub/pdb/validation_reports/r1/4r1p | HTTPS FTP |
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-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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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-MN / #3: 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: 2.25 Å3/Da / Density % sol: 45.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M imidazole hydrochloric acid, 1M sodium citrate tribasic, pH 8.0, 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: 0.97951 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2013 |
Radiation | Monochromator: DCM Si(111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 2.297→50 Å / Num. all: 131054 / Num. obs: 131054 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 28.33 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.144 / Net I/σ(I): 18.333 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.818 / Num. unique all: 6492 / Rsym value: 0.833 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AJT Resolution: 2.297→43.694 Å / FOM work R set: 0.8507 / SU ML: 0.25 / σ(F): 1.35 / Phase error: 22.36 / 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: 83.06 Å2 / Biso mean: 13.18 Å2 / Biso min: 0.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.297→43.694 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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