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- PDB-4zyy: Human GAR transformylase in complex with GAR and (S)-2-({5-[4-(2-... -

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Basic information

Entry
Database: PDB / ID: 4zyy
TitleHuman GAR transformylase in complex with GAR and (S)-2-({5-[4-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]-pyrimidin-6-yl)butyl]thiophene-3-carbonyl}amino)pentanedioic acid (AGF118)
ComponentsTrifunctional purine biosynthetic protein adenosine-3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / gar transformylase / antifolate / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / phosphoribosylamine-glycine ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' XMP biosynthetic process / brainstem development ...adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / phosphoribosylamine-glycine ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' XMP biosynthetic process / brainstem development / 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
Phosphoribosylformylglycinamidine cyclo-ligase / 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 ...Phosphoribosylformylglycinamidine cyclo-ligase / 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 / 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-3YC / GLYCINAMIDE RIBONUCLEOTIDE / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsDeis, S.M. / Dann III, C.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094472 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA166711 United States
CitationJournal: Biochemistry / Year: 2016
Title: Structural and Enzymatic Analysis of Tumor-Targeted Antifolates That Inhibit Glycinamide Ribonucleotide Formyltransferase.
Authors: Deis, S.M. / Doshi, A. / Hou, Z. / Matherly, L.H. / Gangjee, A. / Dann, C.E.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trifunctional purine biosynthetic protein adenosine-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5563
Polymers22,8101
Non-polymers7462
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.005, 75.005, 100.853
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Trifunctional purine biosynthetic protein adenosine-3


Mass: 22810.139 Da / Num. of mol.: 1 / Fragment: gar transformylase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GART, PGFT, PRGS / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: P22102, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-GAR / GLYCINAMIDE RIBONUCLEOTIDE


Mass: 284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N2O8P
#3: Chemical ChemComp-3YC / (S)-2-({5-[4-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]-pyrimidin-6-yl)butyl]thiophene-3-carbonyl}amino)pentanedioic acid


Mass: 461.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 18 % PEG4000, 2 % PEG400, 0.33 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0001 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Aug 24, 2014
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0001 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 28587 / % possible obs: 99.4 % / Redundancy: 9.5 % / Biso Wilson estimate: 19.33 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.021 / Rrim(I) all: 0.067 / Χ2: 0.955 / Net I/av σ(I): 31.987 / Net I/σ(I): 19 / Num. measured all: 270530
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.885.80.48813300.8790.2040.5320.82993.2
1.88-1.926.90.4713820.9120.1850.5070.91698.4
1.92-1.957.80.42313950.9530.160.4531.10699.6
1.95-1.998.60.33814430.9690.1210.360.83299.9
1.99-2.049.10.28714300.980.10.3040.83100
2.04-2.089.50.21714070.990.0740.2290.853100
2.08-2.149.60.17514060.9920.060.1850.897100
2.14-2.199.70.1614110.9930.0540.1690.971100
2.19-2.269.70.13714350.9940.0460.1451.056100
2.26-2.339.90.10814270.9950.0360.1140.728100
2.33-2.419.90.114210.9960.0330.1060.768100
2.41-2.5110.10.08914430.9960.0290.0940.808100
2.51-2.6310.10.0814210.9970.0260.0840.845100
2.63-2.7610.30.07414270.9980.0240.0780.942100
2.76-2.9410.30.06914470.9970.0230.0731.061100
2.94-3.1610.30.06514500.9980.0210.0681.194100
3.16-3.4810.40.06114500.9980.020.0641.294100
3.48-3.9910.50.05414660.9980.0170.0571.17100
3.99-5.0210.40.04914870.9980.0160.0521.04399.9
5.02-509.90.04515090.9980.0150.0480.81896.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X76

4x76
PDB Unreleased entry


Resolution: 1.85→39.832 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1959 1988 7.14 %
Rwork0.1683 25844 -
obs0.1703 27832 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.7 Å2 / Biso mean: 27.8061 Å2 / Biso min: 9.21 Å2
Refinement stepCycle: final / Resolution: 1.85→39.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 50 150 1699
Biso mean--37.36 30.39 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071707
X-RAY DIFFRACTIONf_angle_d1.0562338
X-RAY DIFFRACTIONf_chiral_restr0.046271
X-RAY DIFFRACTIONf_plane_restr0.005307
X-RAY DIFFRACTIONf_dihedral_angle_d12.907640
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8467-1.89290.2726930.22471208130165
1.8929-1.94410.28681360.21441760189693
1.9441-2.00130.21611440.188818732017100
2.0013-2.06590.22561440.184218812025100
2.0659-2.13970.17951480.167918982046100
2.1397-2.22540.17421440.162618622006100
2.2254-2.32660.20491470.159418932040100
2.3266-2.44930.18021460.167418862032100
2.4493-2.60270.2021460.176619032049100
2.6027-2.80360.20321420.188119042046100
2.8036-3.08560.21461430.188219082051100
3.0856-3.53190.23221470.179319322079100
3.5319-4.44890.16181530.146319532106100
4.4489-39.84170.16591550.13961983213897
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)
10.89650.0236-0.46191.05230.0872.49770.1006-0.11460.13970.038-0.0129-0.1185-0.27740.2853-0.07250.1782-0.04620.04280.16950.03030.160340.7847-24.065124.614
22.2687-0.42060.38953.08521.68117.02160.1907-0.4710.38730.4157-0.1501-0.5539-0.41340.4671-0.03180.3226-0.18830.02910.3199-0.03150.330144.4179-15.581530.1046
31.1022-0.4378-0.08921.6374-0.79140.75550.2252-0.16660.64410.4148-0.0526-0.0561-0.75640.0636-0.04820.6347-0.1360.19680.2179-0.02420.556838.8534-4.939325.4436
40.81780.4179-0.54460.5572-0.52841.05550.21730.14070.4281-0.00840.01660.0306-0.5179-0.1689-0.16370.31530.04180.08930.13440.04450.236425.4987-16.953728.0214
51.1411-0.1564-0.22520.67980.40193.46030.05050.02520.12410.04820.0136-0.0974-0.1464-0.0374-0.04360.1247-0.0010.02070.05660.01140.099128.4662-29.103634.6167
61.68661.17810.29576.81540.01984.86910.00160.93190.3923-0.4809-0.20350.8602-0.5649-0.79390.13190.27050.0675-0.01780.38390.03660.225623.8234-25.297612.8921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 808 through 835 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 836 through 855 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 856 through 884 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 885 through 954 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 955 through 992 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 993 through 1007 )A0

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