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- PDB-1rbz: Human GAR Tfase complex structure with polyglutamated 10-(trifluo... -

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Basic information

Entry
Database: PDB / ID: 1rbz
TitleHuman GAR Tfase complex structure with polyglutamated 10-(trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic acid
ComponentsPHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
KeywordsTRANSFERASE / PROTEIN-COFACTOR ANALOGUE COMPLEX
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 / response to inorganic substance / tetrahydrofolate biosynthetic process / cerebellum development / response to organic substance / cerebral cortex development / extracellular exosome / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. ...Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide formyltransferase / Formyl transferase, N-terminal domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KT5 / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, Y. / Desharnais, J. / Boger, D.L. / Wilson, I.A.
CitationJournal: To be Published
Title: Human GAR Tfase complex structure
Authors: Zhang, Y. / Desharnais, J. / Boger, D.L. / Wilson, I.A.
History
DepositionNov 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
B: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4824
Polymers45,3582
Non-polymers2,1242
Water2,756153
1
A: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7412
Polymers22,6791
Non-polymers1,0621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7412
Polymers22,6791
Non-polymers1,0621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.157, 126.157, 93.987
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: Protein PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE / / E.C.2.1.2.2 / GART / GAR transformylase / 5'-phosphoribosylglycinamide transformylase


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.) Homo sapiens (human) / Gene: purN / Plasmid: pet22a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold
References: UniProt: P22102, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-KT5 / N-{4-4-(2,4-DIAMINO-6-OXO-1,6-DIHYDRO-PYRIMIDIN-5-YL)-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXY-ETHYL)-BUT-2-YL-BENZOYL}-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GAMMA-GLUTAMYL-GLUTAMIC ACID


Mass: 1061.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H54F3N9O20
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.71 Å3/Da / Density % sol: 73.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: PEG 1500, Sodium Acetate, pH 4., VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.992 Å
DetectorType: ADSC QUANTUM 9 / Detector: CCD / Date: Jun 14, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.06→47 Å / Num. all: 53508 / Num. obs: 53508 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.15 % / Rsym value: 0.07 / Net I/σ(I): 24.9
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 3.68 % / Mean I/σ(I) obs: 1.71 / Num. unique all: 5186 / Rsym value: 0.614 / % possible all: 96.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NJS

1njs


Resolution: 2.1→47 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2437 -RANDOM
Rwork0.245 ---
all0.246 47964 --
obs0.246 47964 94.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.425 Å2-0.837 Å20 Å2
2---1.425 Å20 Å2
3---2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 121 153 3288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.009
X-RAY DIFFRACTIONr_angle_refined_deg1.49

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