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Yorodumi- PDB-4xb2: Hyperthermophilic archaeal homoserine dehydrogenase mutant in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xb2 | |||||||||
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Title | Hyperthermophilic archaeal homoserine dehydrogenase mutant in complex with NADPH | |||||||||
Components | 319aa long hypothetical homoserine dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / Rossmann fold | |||||||||
Function / homology | Function and homology information homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / NADP binding Similarity search - Function | |||||||||
Biological species | Pyrococcus horikoshii OT3 (archaea) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.43 Å | |||||||||
Authors | Sakuraba, H. / Inoue, S. / Yoneda, K. / Ohshima, T. | |||||||||
Citation | Journal: Sci Rep / Year: 2015 Title: Crystal Structures of a Hyperthermophilic Archaeal Homoserine Dehydrogenase Suggest a Novel Cofactor Binding Mode for Oxidoreductases. Authors: Hayashi, J. / Inoue, S. / Kim, K. / Yoneda, K. / Kawarabayasi, Y. / Ohshima, T. / Sakuraba, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xb2.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xb2.ent.gz | 109.7 KB | Display | PDB format |
PDBx/mmJSON format | 4xb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/4xb2 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xb2 | HTTPS FTP |
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-Related structure data
Related structure data | 4xb1SC 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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Unit cell |
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-Components
#1: Protein | Mass: 36916.895 Da / Num. of mol.: 2 / Mutation: K57A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Gene: PH1075 / Plasmid: pColdI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O58802 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.29 Å3/Da / Density % sol: 46.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEGME2000, citrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 28, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: MicroMax mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.43→50 Å / Num. obs: 25243 / % possible obs: 99 % / Redundancy: 4 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Χ2: 0.747 / Net I/av σ(I): 25.935 / Net I/σ(I): 15 / Num. measured all: 102119 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XB1 Resolution: 2.43→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.433 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.535 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 129.5 Å2 / Biso mean: 36.666 Å2 / Biso min: 12.62 Å2
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Refinement step | Cycle: final / Resolution: 2.43→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.432→2.495 Å / Total num. of bins used: 20
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