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Yorodumi- PDB-6zur: Psychrophilic aromatic amino acids aminotransferase from Psychrob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zur | |||||||||
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Title | Psychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6 cocrystalized with substrate analog - L-p-hydroxyphenyllactic acid | |||||||||
Components | Aminotransferase | |||||||||
Keywords | TRANSFERASE / psychrophilic / aminotranasferase / cold-adapted / enzyme / complex / hydroxyphenyllactic acid / inhibitor | |||||||||
Function / homology | Function and homology information Transferases; Transferring nitrogenous groups; Transaminases / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / pyridoxal phosphate binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Psychrobacter sp. B6 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å | |||||||||
Authors | Bujacz, A. / Rum, J. / Rutkiewicz, M. / Pietrzyk-Brzezinska, A.J. / Bujacz, G. | |||||||||
Funding support | Poland, 1items
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Citation | Journal: Materials (Basel) / Year: 2021 Title: Structural Evidence of Active Site Adaptability towards Different Sized Substrates of Aromatic Amino Acid Aminotransferase from Psychrobacter Sp. B6. Authors: Bujacz, A. / Rum, J. / Rutkiewicz, M. / Pietrzyk-Brzezinska, A.J. / Bujacz, G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6. Authors: Bujacz, A. / Rutkiewicz-Krotewicz, M. / Nowakowska-Sapota, K. / Turkiewicz, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zur.cif.gz | 171.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zur.ent.gz | 136.5 KB | Display | PDB format |
PDBx/mmJSON format | 6zur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zur_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6zur_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6zur_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 6zur_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/6zur ftp://data.pdbj.org/pub/pdb/validation_reports/zu/6zur | HTTPS FTP |
-Related structure data
Related structure data | 6t3vC 6zupC 6zvgC 4rkcS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44199.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter sp. B6 (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: C7E5X4, Transferases; Transferring nitrogenous groups; Transaminases |
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-Non-polymers , 5 types, 320 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-NO3 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.06 Å3/Da / Density % sol: 40.24 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M MgNO3, 20% PEG 2000, HEPES pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2017 / Details: Mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.31→43.65 Å / Num. obs: 31189 / % possible obs: 96.4 % / Redundancy: 3.229 % / Biso Wilson estimate: 44.525 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.11 / Χ2: 0.951 / Net I/σ(I): 9.71 / Num. measured all: 100722 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 4RKC Resolution: 2.31→43.65 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.171 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.058 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.81 Å2 / Biso mean: 44.612 Å2 / Biso min: 21.72 Å2
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Refinement step | Cycle: final / Resolution: 2.31→43.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.369 Å / Rfactor Rfree error: 0
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