+Open data
-Basic information
Entry | Database: PDB / ID: 7b0d | ||||||
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Title | Sugar transaminase from Archaeoglobus veneficus | ||||||
Components | Glutamine--scyllo-inositol transaminase | ||||||
Keywords | TRANSFERASE / aminotransferase / thermostability / catalysis | ||||||
Function / homology | Function and homology information glutamine-scyllo-inositol transaminase / glutamine-scyllo-inositol transaminase activity / L-glutamine:2-oxoglutarate aminotransferase activity Similarity search - Function | ||||||
Biological species | Archaeoglobus veneficus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å | ||||||
Authors | James, P. / Littlechild, J.A. / De Rose, S.A. / Isupov, M.N. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Sugar transaminases from hot environments Authors: James, P. / Littlechild, J.A. / De Rose, S.A. / Isupov, M.N. / Karki, S. / Tabji, A.B. / Garcia-Moyano, A. / Birkeland, N.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7b0d.cif.gz | 377.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b0d.ent.gz | 303.1 KB | Display | PDB format |
PDBx/mmJSON format | 7b0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b0d_validation.pdf.gz | 970.9 KB | Display | wwPDB validaton report |
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Full document | 7b0d_full_validation.pdf.gz | 989.4 KB | Display | |
Data in XML | 7b0d_validation.xml.gz | 41 KB | Display | |
Data in CIF | 7b0d_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/7b0d ftp://data.pdbj.org/pub/pdb/validation_reports/b0/7b0d | HTTPS FTP |
-Related structure data
Related structure data | 7b0mC 3nyuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4280705 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 0 - 367 / Label seq-ID: 28 - 395
NCS ensembles : (Details: Local NCS retraints between domains: 1 2) |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45799.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus veneficus (strain DSM 11195 / SNP6) (archaea) Strain: DSM 11195 / SNP6 / Gene: Arcve_0555 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: F2KQE6, glutamine-scyllo-inositol transaminase |
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-Non-polymers , 6 types, 753 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-PO4 / #5: Chemical | #6: Chemical | ChemComp-TRS / | #7: 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: 2.26 Å3/Da / Density % sol: 45.54 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 4.2 / Details: 0.1 M phosphate/citrate 20 % w/v PEG 6K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 14, 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: 1.27→49.29 Å / Num. obs: 212879 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Redundancy: 5 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.27→1.29 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.352 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 9242 / CC1/2: 0.305 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3nyu Resolution: 1.27→49.287 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.162 / WRfactor Rwork: 0.139 / SU B: 0.838 / SU ML: 0.034 / Average fsc free: 0.913 / Average fsc work: 0.9172 / Cross valid method: FREE R-VALUE / ESU R: 0.042 / ESU R Free: 0.045 Details: Hydrogens have been added in their riding positions
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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 PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.446 Å2
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Refinement step | Cycle: LAST / Resolution: 1.27→49.287 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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