+Open data
-Basic information
Entry | Database: PDB / ID: 5bj3 | ||||||
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Title | THERMUS THERMOPHILUS ASPARTATE AMINOTRANSFERASE TETRA MUTANT 1 | ||||||
Components | PROTEIN (ASPARTATE AMINOTRANSFERASE) | ||||||
Keywords | TRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL ENZYME | ||||||
Function / homology | Function and homology information aspartate-prephenate aminotransferase / aspartate-prephenate aminotransferase activity / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / biosynthetic process / pyridoxal phosphate binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Ura, H. / Nakai, T. / Kawaguchi, S.I. / Miyahara, I. / Hirotsu, K. / Kuramitsu, S. | ||||||
Citation | Journal: J.BIOCHEM.(TOKYO) / Year: 2001 Title: Substrate recognition mechanism of thermophilic dual-substrate enzyme Authors: Ura, H. / Nakai, T. / Kawaguchi, S.I. / Miyahara, I. / Hirotsu, K. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bj3.cif.gz | 287.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bj3.ent.gz | 233.7 KB | Display | PDB format |
PDBx/mmJSON format | 5bj3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bj3_validation.pdf.gz | 413.7 KB | Display | wwPDB validaton report |
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Full document | 5bj3_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 5bj3_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 5bj3_validation.cif.gz | 47.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/5bj3 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/5bj3 | HTTPS FTP |
-Related structure data
Related structure data | 1b5oC 1b5pC 1gc3C 1gc4C 1gckC 5bj4C 1bjwS 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: 42154.969 Da / Num. of mol.: 4 / Mutation: S14D,T16P,K101S,S261R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / Strain (production host): AB1157 / References: UniProt: Q56232, aspartate transaminase #2: Chemical | ChemComp-PLP / #3: 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: 2.88 Å3/Da / Density % sol: 57.3 % |
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Crystal grow | pH: 4.3 / Details: CRYSTALLIZED FROM 30MM AMMONIUM PHOSPHATE, PH 4.3 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 77082 / % possible obs: 78.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2→2.28 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3 / % possible all: 61.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BJW Resolution: 2.2→8 Å / Rfactor Rfree error: 0.0028 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 24.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev Biso : 3.17 Å2 / Rms dev position: 0.076 Å / Weight Biso : 1 / Weight position: 500 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
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Xplor file |
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