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- PDB-1rbm: Human GAR Tfase complex structure with polyglutamated 10-(trifluo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rbm | ||||||
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Title | Human GAR Tfase complex structure with polyglutamated 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid | ||||||
![]() | PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE | ||||||
![]() | TRANSFERASE / PROTEIN-COFACTOR ANALOGUE 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. / Boger, D.L. / Wilson, I.A. | ||||||
![]() | ![]() Title: Human GAR Tfase complex structure Authors: Zhang, Y. / Desharnais, J. / 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 | ![]() | 168.9 KB | Display | ![]() |
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PDB format | ![]() | 134.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rbyC ![]() 1rbzC ![]() 1rc0C ![]() 1rc1C ![]() 1njsS 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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Components
#1: Protein | Mass: 22678.941 Da / Num. of mol.: 2 / Fragment: (residues 808-1010) Source method: isolated from a genetically manipulated source Details: part of Trifunctional purine biosynthetic protein adenosine-3 Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22102, phosphoribosylglycinamide formyltransferase 1 #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.71 Å3/Da / Density % sol: 73.7 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MPD, Calcium cloride, MES, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 9 / Detector: CCD / Date: Apr 20, 2002 / Details: mirror |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→31.47 Å / Num. all: 37921 / Num. obs: 37921 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 2.84 % / Rsym value: 0.064 / Net I/σ(I): 15.76 |
Reflection shell | Resolution: 2.27→2.32 Å / Redundancy: 2.72 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.344 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1NJS Resolution: 2.3→31.47 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.879 / SU B: 4.708 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.005 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→31.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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