+Open data
-Basic information
Entry | Database: PDB / ID: 2vpi | ||||||
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Title | Human GMP synthetase - glutaminase domain | ||||||
Components | GMP SYNTHASE | ||||||
Keywords | LIGASE / GUANINE MONOPHOSPHATE SYNTHETASE / PHOSPHOPROTEIN / GMP SYNTHETASE / GMP BIOSYNTHESIS / GLUTAMINE AMIDOTRANSFERASE / GMPS / CYTOPLASM / ATP-BINDING / PROTO-ONCOGENE / GLUTAMINASE DOMAIN / NUCLEOTIDE-BINDING / PURINE BIOSYNTHESIS / CHROMOSOMAL REARRANGEMENT | ||||||
Function / homology | Function and homology information GMP synthase activity / GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / purine ribonucleoside monophosphate biosynthetic process / purine nucleobase biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / GMP biosynthetic process / Azathioprine ADME / glutamine metabolic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Welin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Welin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Van Der Berg, S. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Human Gmp Synthetase - Glutaminase Domain Authors: Welin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, ...Authors: Welin, M. / Tresaugues, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R.D. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Herman, M.D. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Svensson, L. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vpi.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vpi.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/2vpi ftp://data.pdbj.org/pub/pdb/validation_reports/vp/2vpi | HTTPS FTP |
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-Related structure data
Related structure data | 1gpmS S: Starting model for refinement |
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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: Ens-ID: 1 / Refine code: 1
NCS oper: (Code: given Matrix: (0.8458, -0.03098, 0.5326), Vector: |
-Components
#1: Protein | Mass: 23819.168 Da / Num. of mol.: 2 / Fragment: GLUTAMINASE DOMAIN, RESIDUES 25-219 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PNIC-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 PRARE References: UniProt: P49915, GMP synthase (glutamine-hydrolysing) #2: Water | ChemComp-HOH / | Sequence details | CONTAINS AN N-TERMINAL HEXAHISTID | |
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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: 2.38 Å3/Da / Density % sol: 40.11 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.2 M AMMONIUM ACETATE 0.1 M BIS-TRIS PH 5.5 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 2, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 14466 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4.13 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.52 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.88 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.96 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GPM Resolution: 2.4→19.77 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.854 / SU B: 8.472 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.621 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 77-85 IN CHAIN A AND 77-86 IN CHAIN B ARE DISORDERED. MET 24 IS FROM HIS TAG AND CORRESPONDS TO A TYR IN BIOLOGICAL SEQUENCE.
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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: 16.35 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→19.77 Å
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Refine LS restraints |
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