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- PDB-1rc0: Human GAR Tfase complex structure with polyglutamated 10-(trifluo... -

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Basic information

Entry
Database: PDB / ID: 1rc0
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


phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / phosphoribosylamine-glycine ligase activity / brainstem development / 'de novo' XMP biosynthetic process ...phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / phosphoribosylamine-glycine ligase activity / brainstem development / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / purine nucleotide biosynthetic process / GMP biosynthetic process / 'de novo' IMP biosynthetic process / cerebellum development / cerebral cortex development / extracellular exosome / ATP binding / metal ion binding / cytosol
Similarity search - Function
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 / 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 / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylformylglycinamidine cyclo-ligase / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / 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: 2.05 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

Downloads & links

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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
Water2,792155
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)126.305, 126.305, 93.598
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


Mass: 18.015 Da / Num. of mol.: 155 / 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: 4.2
Details: isoproponal, Calcium Cloride, Sodum Acetate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 9 / Detector: CCD / Date: Apr 19, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.05→35.58 Å / Num. all: 54005 / Num. obs: 54005 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.55 % / Rsym value: 0.05 / Net I/σ(I): 26.7
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.58 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2687 / Rsym value: 0.475 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NJS

1njs


Resolution: 2.05→35.58 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.237 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24257 2556 5 %RANDOM
Rwork0.22217 ---
all0.22319 50919 --
obs0.22319 50919 94.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.168 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20.1 Å20 Å2
2--0.2 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.05→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 76 155 3245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9824268
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9215398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.21370
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2181
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.471.51992
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92123216
X-RAY DIFFRACTIONr_scbond_it1.65231148
X-RAY DIFFRACTIONr_scangle_it2.884.51052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.277 194
Rwork0.247 3369
obs-3369
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2594-1.1646-0.3451.80190.12251.1688-0.0425-0.33270.29030.19030.080.0788-0.2759-0.1848-0.03740.09170.0264-0.02210.0922-0.00740.039143.215141.160724.6129
22.3424-1.19610.07881.93830.23991.4903-0.02350.00830.0551-0.1430.0572-0.32930.13570.2131-0.03360.0529-0.0130.01310.00440.00380.043873.936617.864722.3049
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2001 - 200
2X-RAY DIFFRACTION2BB1 - 2001 - 200

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