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Open data
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Basic information
Entry | Database: PDB / ID: 1men | ||||||
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Title | complex structure of human GAR Tfase and substrate beta-GAR | ||||||
![]() | Phosphoribosylglycinamide formyltransferase | ||||||
![]() | TRANSFERASE / purine biosynthesis / substrate-enzyme complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Desharnais, J. / Greasley, S.E. / Beardsley, G.P. / Boger, D.L. / Wilson, I.A. | ||||||
![]() | ![]() Title: Crystal structures of human GAR Tfase of low and high pH and with substrate beta-GAR Authors: Zhang, Y. / Desharnais, J. / Greasley, S.E. / Beardsley, G.P. / Boger, D.L. / Wilson, I.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128 KB | Display | ![]() |
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PDB format | ![]() | 100.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 561.6 KB | Display | ![]() |
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Full document | ![]() | 553.9 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mejSC ![]() 1meoC 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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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24122.635 Da / Num. of mol.: 3 / Fragment: Residues 810-1010 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22102, phosphoribosylglycinamide formyltransferase 1 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG4000, PEG400, NaCl, Tris pH 8.5, 2mM beta-GAR, VAPOR DIFFUSION, SITTING DROP, temperature 282K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 4, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→43.02 Å / Num. all: 38266 / Num. obs: 35682 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.23→2.3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.54 / Num. unique all: 3349 / % possible all: 86.4 |
Reflection | *PLUS Lowest resolution: 43 Å / Num. obs: 38266 / % possible obs: 98.5 % / Redundancy: 3.78 % / Num. measured all: 144600 |
Reflection shell | *PLUS % possible obs: 86.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MEJ Resolution: 2.23→35.28 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 43.9 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.35 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→35.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.37 Å / Rfactor Rfree error: 0.016
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Xplor file |
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Refinement | *PLUS Lowest resolution: 43 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.22 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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