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Yorodumi- PDB-4chi: (R)-selective amine transaminase from Aspergillus fumigatus at 1.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4chi | ||||||
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Title | (R)-selective amine transaminase from Aspergillus fumigatus at 1.27 A resolution | ||||||
Components | BRANCHED-CHAIN AMINO ACID AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information Transferases; Transferring nitrogenous groups; Transaminases / carboxylic acid metabolic process / transaminase activity Similarity search - Function | ||||||
Biological species | ASPERGILLUS FUMIGATUS (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.27 Å | ||||||
Authors | Thomsen, M. / Palm, G.J. / Hinrichs, W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Crystallographic Characterization of the (R)-Selective Amine Transaminase from Aspergillus Fumigatus. Authors: Thomsen, M. / Skalden, L. / Palm, G.J. / Hohne, M. / Bornscheuer, U.T. / Hinrichs, W. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Crystallization and Preliminary X-Ray Diffraction Studies of the (R)-Selective Amine Transaminase from Aspergillus Fumigatus Authors: Thomsen, M. / Skalden, L. / Palm, G.J. / Hoehne, M. / Bornscheuer, U.T. / Hinrichs, W. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4chi.cif.gz | 339.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4chi.ent.gz | 292.4 KB | Display | PDB format |
PDBx/mmJSON format | 4chi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/4chi ftp://data.pdbj.org/pub/pdb/validation_reports/ch/4chi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.864, -0.007, -0.504), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37192.344 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Strain: AF293 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q4WH08, Transferases; Transferring nitrogenous groups; Transaminases, beta-alanine-pyruvate transaminase |
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-Non-polymers , 7 types, 1047 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-K / #7: Chemical | ChemComp-CL / #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | PYRIDOXAL-5'-PHOSPHATE (PLP): COVALENTLY |
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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: 2.9 Å3/Da / Density % sol: 58 % Description: THE DATA SET AT WAVELENGTH 0.9184 A WAS USED FOR DATA COLLECTION STATISTICS AND REFINEMENT. THE DATA SET AT WAVELENGTH 1.7712 A WAS USED FOR S-SAD AND ANOMALOUS MAP CALCULATION. |
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Crystal grow | pH: 7.5 / Details: 20 MM TRICINE PH 7.5, 0.01 MM PLP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841,1.7712 | |||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2013 / Details: MIRROR | |||||||||
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.27→50 Å / Num. obs: 426722 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.38 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.2 | |||||||||
Reflection shell | Resolution: 1.27→1.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.27→47.88 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.972 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. OCCUPANCIES OF ANOMALOUS SCATTERERS WERE SET TO ACCOMMODATE NORMAL AND ANOMALOUS MAPS, OCCASIONALLY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. OCCUPANCIES OF ANOMALOUS SCATTERERS WERE SET TO ACCOMMODATE NORMAL AND ANOMALOUS MAPS, OCCASIONALLY RESULTING IN UNINTERPRETABLE B-FACTORS.
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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 mean: 16.118 Å2
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Refinement step | Cycle: LAST / Resolution: 1.27→47.88 Å
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