+Open data
-Basic information
Entry | Database: PDB / ID: 1meo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | human glycinamide ribonucleotide Transformylase at pH 4.2 | |||||||||
Components | Phosphoribosylglycinamide formyltransferase | |||||||||
Keywords | TRANSFERASE / purine biosynthesis | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | |||||||||
Authors | Zhang, Y. / Desharnais, J. / Greasley, S.E. / Beardsley, G.P. / Boger, D.L. / Wilson, I.A. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1meo.cif.gz | 54.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1meo.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 1meo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/1meo ftp://data.pdbj.org/pub/pdb/validation_reports/me/1meo | HTTPS FTP |
---|
-Related structure data
Related structure data | 1mejSC 1menC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22678.941 Da / Num. of mol.: 1 / Fragment: Residues 808-1010 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GART / Plasmid: pet22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) gold References: UniProt: P22102, phosphoribosylglycinamide formyltransferase 1 |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.4 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 1.9-2.1M Ammonium Sulfate, 100mM Na Acetate pH 4.2-4.6, VAPOR DIFFUSION, SITTING DROP, temperature 282K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.976 Å |
Detector | Type: ADSC QUANTUM 9 / Detector: CCD / Date: Nov 16, 2001 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→43.92 Å / Num. obs: 40379 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.65 / Num. unique all: 16675 / % possible all: 99 |
Reflection | *PLUS Lowest resolution: 46 Å / % possible obs: 98.7 % / Redundancy: 4.15 % / Num. measured all: 167456 |
Reflection shell | *PLUS % possible obs: 99 % / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MEJ Resolution: 1.72→43.85 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.849 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.691 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→43.85 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.72→1.765 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 46 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.225 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|