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Open data
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Basic information
Entry | Database: PDB / ID: 2v9y | ||||||
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Title | Human aminoimidazole ribonucleotide synthetase | ||||||
![]() | PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE | ||||||
![]() | LIGASE / MULTIFUNCTIONAL ENZYME / STRUCTURAL GENOMICS CONSORTIUM / NUCLEOTIDE-BINDING / PURINE BIOSYNTHESIS / SGC / AIRS / GART / TRANSFERASE / ATP-BINDING / AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE / PHOSPHORYLATION / PURINE METABOLISM / STRUCTURAL GENOMICS | ||||||
Function / homology | ![]() phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / adenine biosynthetic process / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / phosphoribosylglycinamide formyltransferase 1 / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' XMP biosynthetic process / brainstem development ...phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / adenine biosynthetic process / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / phosphoribosylglycinamide formyltransferase 1 / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' XMP biosynthetic process / brainstem development / Purine ribonucleoside monophosphate biosynthesis / glycine metabolic process / 'de novo' AMP biosynthetic process / GMP biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / : / tetrahydrofolate biosynthetic process / cerebellum development / : / cerebral cortex development / extracellular exosome / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Welin, M. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Herman, M.D. / Edwards, A.M. / Flodin, S. ...Welin, M. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Herman, M.D. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structural Studies of Tri-Functional Human Gart. Authors: Welin, M. / Grossmann, J.G. / Flodin, S. / Nyman, T. / Stenmark, P. / Tresaugues, L. / Kotenyova, T. / Johansson, I. / Nordlund, P. / Lehtio, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.5 KB | Display | ![]() |
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PDB format | ![]() | 103.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.1 KB | Display | ![]() |
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Full document | ![]() | 454.9 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qk4C ![]() 1cliS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.02232, 0.9998, 0.001274), Vector: |
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Components
#1: Protein | Mass: 35830.016 Da / Num. of mol.: 2 / Fragment: RESIDUES 467-794 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22102, phosphoribosylformylglycinamidine cyclo-ligase #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | SULFATE ION (SO4): FLEXIBLE REGION BETWEEN RESIDUE 770 AND 773 IN BOTH A AND B. | Sequence details | SEQUENCE CONTAINED AN N-TERMINAL HEXAHISTID | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE |
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Crystal grow | pH: 5.2 Details: 0.1 M BIS-TRIS PH 5.2, 27% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.2 MG/ML OF CHYMOTRYPSIN WAS ADDED PRIOR TO CRYSTALLISATION. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 12, 2007 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→15 Å / Num. obs: 38171 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 14.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 8.06 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CLI Resolution: 2.1→14.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.202 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PROTEIN WAS CO CRYSTALLIZED WITH CHYMOTRYPSIN AND THE MOST PROBABLE SEQUENCE IN THE CRYSTAL IS KVDLGGFAGLFDLKAAGFKDPLLA SGTDGVGTKL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PROTEIN WAS CO CRYSTALLIZED WITH CHYMOTRYPSIN AND THE MOST PROBABLE SEQUENCE IN THE CRYSTAL IS KVDLGGFAGLFDLKAAGFKDPLLA SGTDGVGTKL KIAQLCNKHD TIGQDLVAMC VNDILAQGAE PLFFLDYFSC GKLDLSVTEA VVAGIAKACG KAGCALLGGE TAEMPDMYPP GEYDLAGFAV GAMERDQKLP HLERITEGDV VVGIASSGLH SNGFSLVRKI VAKSSLQYSS PAPDGCGDQT LGDLLLTPTR IYSHSLLPVL RSGHVKAFAH ITGGGLLENI PRVLPEKLGV DLDAQTWRIP RVFSWLQQEG HLSEEEMART FNCGVGAVLV VSKEQTEQIL RGIQQHKEEA WVIGSVVARA EGSPRVKVKN LIESMQINGS VLKN
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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: 32.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→14.99 Å
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Refine LS restraints |
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