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Yorodumi- PDB-5mqz: Archaeal branched-chain amino acid aminotransferase from Archaeog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mqz | ||||||
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Title | Archaeal branched-chain amino acid aminotransferase from Archaeoglobus fulgidus; holoform | ||||||
Components | Putative branched-chain-amino-acid aminotransferase | ||||||
Keywords | TRANSFERASE / branch-chain transaminase / thermophilic archaea / 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: 2.1 Å | ||||||
Authors | James, P. / Isupov, M.N. / Sayer, C. / Littlechild, J.A. / 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 Archaea Geoglobus acetivorans and Archaeoglobus 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 | 5mqz.cif.gz | 379.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mqz.ent.gz | 310.5 KB | Display | PDB format |
PDBx/mmJSON format | 5mqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/5mqz ftp://data.pdbj.org/pub/pdb/validation_reports/mq/5mqz | HTTPS FTP |
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-Related structure data
Related structure data | 5cm0C 5e25C 5mr0C 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
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 32631.131 Da / Num. of mol.: 6 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 , 5 types, 678 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.17 Å3/Da / Density % sol: 43.33 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 6.5 Details: 50 % PEG 200,0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium cacodylate |
-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: 2.1→69.56 Å / Num. obs: 99985 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.135 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.27 / Mean I/σ(I) obs: 0.8 / CC1/2: 0.292 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EIY Resolution: 2.1→66.86 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.631 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.186
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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: 45.898 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→66.86 Å
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Refine LS restraints |
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