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- PDB-4zyz: Human GAR transformylase in complex with GAR and (S)-2-(7-(2-Amin... -

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Basic information

Entry
Database: PDB / ID: 4zyz
TitleHuman GAR transformylase in complex with GAR and (S)-2-(7-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)heptanamido)pentanedioic acid (AGF145)
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 / purine nucleotide biosynthetic process / GMP 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 / 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-3YD / GLYCINAMIDE RIBONUCLEOTIDE / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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)23,5023
Polymers22,8101
Non-polymers6922
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.501, 75.501, 101.111
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-3YD / (S)-2-(7-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)heptanamido)pentanedioic acid


Mass: 407.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H25N5O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 3.89 Å3/Da / Density % sol: 68.35 %
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: 1.6→50 Å / Num. obs: 44634 / % possible obs: 99.5 % / Redundancy: 9.6 % / Biso Wilson estimate: 13.72 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.021 / Rrim(I) all: 0.066 / Χ2: 0.934 / Net I/av σ(I): 32.129 / Net I/σ(I): 18.8 / Num. measured all: 428756
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.634.60.47820930.840.2270.5330.6995.3
1.63-1.666.20.46322010.90.1910.5030.69599.3
1.66-1.698.10.43222200.9320.1580.4610.673100
1.69-1.729.10.36422320.9660.1260.3850.698100
1.72-1.769.60.32322090.9710.1090.3410.743100
1.76-1.89.80.26722250.9780.0890.2810.814100
1.8-1.859.90.22821920.9870.0760.241.016100
1.85-1.9100.17622210.9910.0580.1850.858100
1.9-1.95100.1422170.9940.0460.1470.927100
1.95-2.0210.10.11822010.9950.0390.1240.984100
2.02-2.0910.20.09922290.9970.0320.1041.072100
2.09-2.1710.30.0822610.9980.0260.0840.949100
2.17-2.2710.30.07622370.9970.0250.081.024100
2.27-2.3910.40.0722380.9970.0230.0730.985100
2.39-2.5410.50.06722390.9980.0220.0711.037100
2.54-2.7410.60.06522660.9980.0210.0681.082100
2.74-3.0110.60.06222530.9980.020.0661.189100
3.01-3.4510.70.05622880.9980.0180.0591.121100
3.45-4.3410.60.04822920.9980.0160.0510.91899.9
4.34-50100.04523200.9980.0150.0480.79295.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIXphenix.refine 1.9refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X77

4x77
PDB Unreleased entry


Resolution: 1.6→39.995 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1876 2004 4.58 %
Rwork0.1646 41762 -
obs0.1656 43766 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.24 Å2 / Biso mean: 21.3294 Å2 / Biso min: 7.1 Å2
Refinement stepCycle: final / Resolution: 1.6→39.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 47 203 1753
Biso mean--30 28.36 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061702
X-RAY DIFFRACTIONf_angle_d1.1852328
X-RAY DIFFRACTIONf_chiral_restr0.046270
X-RAY DIFFRACTIONf_plane_restr0.005307
X-RAY DIFFRACTIONf_dihedral_angle_d13.626635
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 (%)
1.5958-1.63570.2266990.19072135223470
1.6357-1.680.23261440.18382930307498
1.68-1.72940.19561420.176230193161100
1.7294-1.78520.18921450.170330193164100
1.7852-1.8490.16171460.167230343180100
1.849-1.92310.18991460.158530293175100
1.9231-2.01060.18381450.162230113156100
2.0106-2.11660.19971480.161930493197100
2.1166-2.24920.15731470.159330633210100
2.2492-2.42280.191440.163930613205100
2.4228-2.66660.20161500.173930683218100
2.6666-3.05230.23231470.182230703217100
3.0523-3.84510.19481450.165631343279100
3.8451-40.00740.15031560.14413140329697
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)
10.8415-0.0811-0.06660.41490.18592.30760.03430.20470.2429-0.35440.0025-0.0741-0.27360.04680.00640.2372-0.04460.04050.158-0.01770.1398-34.502125.418824.5597
21.87090.1964-1.62980.7193-0.27953.98440.06360.11020.1266-0.2221-0.04010.0611-0.2733-0.3090.01320.14620.0132-0.00290.1075-0.02580.1238-45.380222.164926.9025
31.57320.5799-0.29830.6136-0.64972.424-0.05520.23660.5237-0.50290.03850.0318-0.44360.1468-0.03240.3941-0.04480.03770.15670.03960.2417-35.95330.698620.5639
41.101-0.40380.40650.62410.1860.5923-0.03220.24190.5062-0.38020.0878-0.3937-0.4390.60410.00090.2912-0.21080.15060.322-0.08360.4024-23.740430.742525.5445
50.9321-0.0620.1380.52980.35390.96890.1257-0.02980.1985-0.16630.1086-0.3659-0.19990.4602-0.09540.1403-0.0790.04830.247-0.07850.2117-26.576122.322628.583
60.547-0.1308-0.10880.61810.53991.08990.001-0.10780.08440.00130.084-0.1657-0.04840.2563-0.08140.0917-0.01940.00250.1398-0.02250.1251-28.34589.749819.9059
70.58480.0345-0.20310.4381-0.19971.9892-0.04830.01660.0461-0.08720.0448-0.01790.0897-0.1620.0070.1162-0.0010.00230.0942-0.01130.0855-38.27634.797111.7213
80.3848-0.0614-0.2210.33790.41542.02250.0238-0.00810.13640.02440.0366-0.029-0.0791-0.0718-0.03820.0964-0.0070.01120.0862-0.00620.1049-40.303613.389518.4671
93.507-1.3936-0.25573.87910.23231.7433-0.1783-0.4257-0.25830.46670.0016-0.33360.430.42940.10730.27560.0637-0.00810.29750.03550.2149-33.52077.403437.9112
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 968 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 969 through 992 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 993 through 1007 )A0

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