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- PDB-4zyw: Human GAR transformylase in complex with GAR and N-({5-[(2-amino-... -

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Basic information

Entry
Database: PDB / ID: 4zyw
TitleHuman GAR transformylase in complex with GAR and N-({5-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)propyl]thiophen-2-yl}carbonyl)-L-glutamic acid (AGF94)
ComponentsTrifunctional purine biosynthetic protein adenosine-3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / gar transformylase / antifolate / TRANSFERASE-TRANSFERASE INHIBITOR 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 / : / tetrahydrofolate biosynthetic process / cerebellum development / : / 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-G94 / GLYCINAMIDE RIBONUCLEOTIDE / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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)23,5423
Polymers22,8101
Non-polymers7322
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.256, 75.256, 100.621
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 / Glycineamide ribonucleotide


Mass: 284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13N2O8P
#3: Chemical ChemComp-G94 / N-({5-[3-(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-6-yl)propyl]thiophen-2-yl}carbonyl)-L-glutamic acid


Mass: 447.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N5O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.86 Å3/Da / Density % sol: 68.17 %
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: Apr 6, 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: 2.05→50 Å / Num. obs: 21298 / % possible obs: 99.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 24.46 Å2 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.033 / Rrim(I) all: 0.108 / Χ2: 0.938 / Net I/av σ(I): 23.162 / Net I/σ(I): 10.2 / Num. measured all: 220599
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.096.70.54410370.8970.2060.5840.897.3
2.09-2.127.60.53610020.9330.1940.5710.87698.9
2.12-2.168.60.54310780.9240.1880.5750.91399.9
2.16-2.219.50.53510520.9430.1780.5641.086100
2.21-2.2610.20.46310290.9630.150.4870.997100
2.26-2.3110.80.41810480.9670.1330.4390.877100
2.31-2.37110.34710690.9750.1090.3640.873100
2.37-2.4311.10.32710590.9770.1030.3430.902100
2.43-2.511.10.28410460.9810.0890.2980.946100
2.5-2.5811.10.2410500.9890.0750.2521.042100
2.58-2.6811.10.18310560.9920.0570.1910.774100
2.68-2.7811.10.15610710.9930.0490.1640.797100
2.78-2.9111.10.1310570.9950.0410.1360.837100
2.91-3.0611.10.1110620.9960.0350.1160.922100
3.06-3.25110.09310780.9960.0290.0970.96100
3.25-3.5111.10.08310680.9950.0260.0871.002100
3.51-3.86110.07910770.9960.0250.0831.097100
3.86-4.4210.90.07210880.9970.0230.0751.016100
4.42-5.5610.80.06711040.9970.0220.0710.952100
5.56-5010.10.06811670.9970.0220.0711.03498.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASER2.5.6phasing
PHENIXphenix.refine 1.9refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X72

4x72
PDB Unreleased entry


Resolution: 2.05→39.825 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 2004 9.63 %
Rwork0.1616 18815 -
obs0.1654 20819 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.07 Å2 / Biso mean: 35.249 Å2 / Biso min: 11.97 Å2
Refinement stepCycle: final / Resolution: 2.05→39.825 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 49 104 1648
Biso mean--45.4 31.97 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081621
X-RAY DIFFRACTIONf_angle_d1.1372211
X-RAY DIFFRACTIONf_chiral_restr0.046261
X-RAY DIFFRACTIONf_plane_restr0.004286
X-RAY DIFFRACTIONf_dihedral_angle_d13.708595
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 (%)
2.0459-2.09710.24721070.1978986109373
2.0971-2.15380.2391390.19171265140494
2.1538-2.21720.20561460.187413471493100
2.2172-2.28870.21521440.185813791523100
2.2887-2.37050.261440.171413431487100
2.3705-2.46540.231470.179313571504100
2.4654-2.57760.21251440.175213611505100
2.5776-2.71350.19771430.18213721515100
2.7135-2.88340.22471420.18413761518100
2.8834-3.1060.23351480.187413791527100
3.106-3.41840.22361520.177213841536100
3.4184-3.91260.20031450.146313881533100
3.9126-4.92810.14431500.118113991549100
4.9281-39.83250.17371530.13931479163299
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)
11.9882-0.6617-0.50341.4854-0.05882.14560.2357-0.1934-0.50690.0388-0.03170.44780.7333-0.3527-0.22470.3347-0.0997-0.12760.24440.03550.3529-1.598582.208126.7601
21.0697-1.56592.26133.8444-4.90849.34210.0898-0.3101-0.0903-0.08350.15120.4431-0.007-0.4222-0.25680.2081-0.0432-0.05860.2801-0.01070.2285-4.378792.8814124.9618
31.6472-1.4934-0.37313.529-0.83745.78480.0876-0.3935-0.5550.2224-0.11730.95520.6462-0.7172-0.07340.333-0.1938-0.07660.45080.11070.4938-7.037580.9794130.5947
42.3593-0.489-0.4050.21150.52231.82820.2435-0.2855-1.15070.2114-0.05630.25591.1444-0.0786-0.30810.7481-0.1387-0.31270.29050.10.8938-0.759570.0442125.9703
52.1352-1.08550.52821.09320.94372.90890.3359-0.004-0.8543-0.11670.10840.10480.90110.1609-0.24520.524-0.0065-0.21730.1869-0.03510.46345.356876.8182123.0469
62.18580.41111.16931.99111.13373.03570.2050.1837-0.4321-0.02550.00430.02460.59260.198-0.20580.23230.0438-0.03670.1363-0.02650.196115.208485.1901131.5575
71.84230.08740.61381.5189-0.14764.29610.0462-0.0235-0.12780.06540.0090.16260.01670.0053-0.03040.14450.0089-0.00820.0922-0.00620.12459.207394.3793135.1895
88.46240.5648-1.03125.3352-0.18845.5438-0.11351.4332-0.7498-0.7425-0.2741-0.5620.51560.87290.28390.38810.07470.03860.4385-0.06670.263713.24290.8528113.2894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 808 through 818 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 819 through 835 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 836 through 855 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 856 through 884 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 885 through 906 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 907 through 954 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 955 through 992 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 993 through 1007 )A0

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