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Yorodumi- PDB-5mr0: Thermophilic archaeal branched-chain amino acid transaminases fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mr0 | ||||||
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Title | Thermophilic archaeal branched-chain amino acid transaminases from Geoglobus acetivorans and Archaeoglobus fulgidus: biochemical and structural characterisation | ||||||
Components | (Putative branched-chain-amino-acid ...) x 2 | ||||||
Keywords | TRANSFERASE / Thermophilic archaea / branch-chain transaminases / substrate specificity | ||||||
Function / homology | Function and homology information L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Isupov, M.N. / Littlechild, J.A. / James, P. / Sayer, C. / Sutter, J.M. / Schmidt, M. / Schoenheit, P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Front Bioeng Biotechnol / Year: 2019 Title: Thermostable Branched-Chain Amino Acid Transaminases From the ArchaeaGeoglobus acetivoransandArchaeoglobus fulgidus: Biochemical and Structural Characterization. Authors: Isupov, M.N. / Boyko, K.M. / Sutter, J.M. / James, P. / Sayer, C. / Schmidt, M. / Schonheit, P. / Nikolaeva, A.Y. / Stekhanova, T.N. / Mardanov, A.V. / Ravin, N.V. / Bezsudnova, E.Y. / ...Authors: Isupov, M.N. / Boyko, K.M. / Sutter, J.M. / James, P. / Sayer, C. / Schmidt, M. / Schonheit, P. / Nikolaeva, A.Y. / Stekhanova, T.N. / Mardanov, A.V. / Ravin, N.V. / Bezsudnova, E.Y. / Popov, V.O. / Littlechild, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mr0.cif.gz | 387.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mr0.ent.gz | 316.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mr0 ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mr0 | HTTPS FTP |
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-Related structure data
Related structure data | 5cm0C 5e25C 5mqzC 2eiyS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 1 - 290 / Label seq-ID: 1 - 290
NCS ensembles :
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-Components
-Putative branched-chain-amino-acid ... , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 32403.014 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea) Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 Gene: ilvE, AF_0933 / Production host: Escherichia coli (E. coli) References: UniProt: O29329, branched-chain-amino-acid transaminase #2: Protein | | Mass: 32631.131 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (archaea) Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126 Gene: ilvE, AF_0933 / Production host: Escherichia coli (E. coli) References: UniProt: O29329, branched-chain-amino-acid transaminase |
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-Non-polymers , 6 types, 757 molecules
#3: Chemical | ChemComp-PXG / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Chemical | ChemComp-EDO / | #8: 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: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6.5 Details: 0.1 M Sodium cacodylate, 0.2 M Magnesium chloride hexahydrate, 50 % v/v PEG 200, 5mM gabaculine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→67.13 Å / Num. obs: 119864 / % possible obs: 99 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.98→2.01 Å / Redundancy: 4.7 % / Rmerge(I) obs: 2.07 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.249 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2eiy Resolution: 1.98→64.72 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.512 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.156
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.134 Å2
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Refinement step | Cycle: 1 / Resolution: 1.98→64.72 Å
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Refine LS restraints |
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