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Yorodumi- PDB-2vd3: The structure of histidine inhibited HisG from Methanobacterium t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vd3 | ||||||
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Title | The structure of histidine inhibited HisG from Methanobacterium thermoautotrophicum | ||||||
Components | ATP PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / METAL-BINDING / GLYCOSYLTRANSFERASE / HISG / HISTIDINE / MAGNESIUM / HISTIDINE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS / ATP PHOSPHORIBOSYL TRANSFERASE | ||||||
Function / homology | Function and homology information ATP phosphoribosyltransferase / ATP phosphoribosyltransferase activity / L-histidine biosynthetic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | METHANOBACTERIUM THERMOAUTOTROPHICUM (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.45 Å | ||||||
Authors | Lohkamp, B. / Schweikert, T. / Lapthorn, A.J. | ||||||
Citation | Journal: To be Published Title: The Structure of Histidine Inhibited Hisg from Methanobacterium Thermoautotrophicum Authors: Lohkamp, B. / Schweikert, T. / Lapthorn, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vd3.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vd3.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 2vd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vd3_validation.pdf.gz | 492.7 KB | Display | wwPDB validaton report |
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Full document | 2vd3_full_validation.pdf.gz | 496.7 KB | Display | |
Data in XML | 2vd3_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 2vd3_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/2vd3 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/2vd3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 1 - 287 / Label seq-ID: 3 - 289
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31338.990 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-287 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHANOBACTERIUM THERMOAUTOTROPHICUM (archaea) Strain: DELTAH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O27550, ATP phosphoribosyltransferase |
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-Non-polymers , 7 types, 80 molecules
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-MPD / ( #7: Chemical | ChemComp-MRD / ( | #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: 2.34 Å3/Da / Density % sol: 46.97 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Type: SRS / Wavelength: 1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 10000 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.05 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.45→45 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 23.662 / SU ML: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 2.483 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.15 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→45 Å
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Refine LS restraints |
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