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

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Basic information

Entry
Database: PDB / ID: 4zyv
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)butyl]thiophen-2-yl}carbonyl)-L-glutamic acid (AGF71)
ComponentsTrifunctional purine biosynthetic protein adenosine-3
Keywordstransferase/transferase inhibitor / gar transformylase / antifolate / TRANSFERASE / 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-G71 / GLYCINAMIDE RIBONUCLEOTIDE / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.053 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 / Refinement description / Category: pdbx_audit_support / software / 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
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.203, 75.203, 100.626
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 (UNP residues 808-1010)
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-G71 / N-({5-[4-(2-amino-4-oxo-4,7-dihydro-1H-pyrrolo[2,3-d]pyrimidin-6-yl)butyl]thiophen-2-yl}carbonyl)-L-glutamic 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.: 119 / 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: 3.59 Å3/Da / Density % sol: 65.7 %
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: 21095 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 24.83 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.031 / Rrim(I) all: 0.101 / Χ2: 0.951 / Net I/av σ(I): 24.248 / Net I/σ(I): 10.4 / Num. measured all: 222995
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.097.70.53610210.8910.1990.5740.9598.7
2.09-2.128.80.54510380.9270.1930.5791.10499.9
2.12-2.169.50.45810420.9490.1560.4840.977100
2.16-2.2110.40.4410420.9610.1440.4640.88100
2.21-2.2610.70.38310240.9740.1220.4020.958100
2.26-2.31110.36910340.9740.1160.3870.942100
2.31-2.3711.10.3210550.9810.1010.3360.962100
2.37-2.43110.2810400.9840.0880.2930.977100
2.43-2.511.10.23910630.9870.0750.2511.001100
2.5-2.5811.10.17810350.9930.0560.1870.751100
2.58-2.6811.10.15510460.9940.0480.1620.773100
2.68-2.7811.10.13610650.9950.0430.1430.8100
2.78-2.9111.10.10910320.9960.0340.1140.829100
2.91-3.06110.09510530.9970.030.10.907100
3.06-3.25110.08210590.9970.0260.0870.941100
3.25-3.51110.07810520.9960.0250.0821.053100
3.51-3.86110.07410760.9960.0240.0771.136100
3.86-4.4210.90.06710780.9970.0210.071.049100
4.42-5.5610.70.06510930.9960.0210.0691.028100
5.56-50100.05911470.9980.0190.0621.03398.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXphenix.refine 1.9refinement
PDB_EXTRACT3.14data extraction
PHASER2.5.6phasing
Coot0.7.1model building
SCALEPACKdata scaling
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MEJ

1mej


Resolution: 2.053→39.816 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1923 1989 9.69 %Random
Rwork0.1655 18537 --
obs0.1681 20526 97.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.35 Å2 / Biso mean: 35.8752 Å2 / Biso min: 11.36 Å2
Refinement stepCycle: final / Resolution: 2.053→39.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 50 119 1669
Biso mean--44.64 33.58 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071604
X-RAY DIFFRACTIONf_angle_d1.0712183
X-RAY DIFFRACTIONf_chiral_restr0.042259
X-RAY DIFFRACTIONf_plane_restr0.005280
X-RAY DIFFRACTIONf_dihedral_angle_d13.848591
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 (%)
2.0526-2.10390.2362910.1897930102169
2.1039-2.16080.24461360.19851263139994
2.1608-2.22440.25621420.188213301472100
2.2244-2.29620.20461420.184713341476100
2.2962-2.37820.24481460.173813451491100
2.3782-2.47340.21891460.185913451491100
2.4734-2.5860.22571440.17413551499100
2.586-2.72230.23211450.187413521497100
2.7223-2.89280.22231470.193313551502100
2.8928-3.11610.21511500.187413571507100
3.1161-3.42950.21451460.174713661512100
3.4295-3.92540.17831420.154413761518100
3.9254-4.94410.13171520.124713811533100
4.9441-39.82320.14661600.14611448160898
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)
14.5692-0.76291.65641.57570.33974.58310.1035-0.0633-0.80520.18570.1258-0.02870.53220.1539-0.23880.33690.0082-0.01170.1394-0.04250.3035-1.234238.467860.8894
21.85120.98460.73141.34950.39592.26990.06140.2775-0.6111-0.07840.2872-0.67590.36580.7147-0.12320.22080.12380.00130.3526-0.1380.40910.993946.260860.8565
31.73060.20350.62611.99370.37383.4544-0.0167-0.0624-0.1950.04890.0929-0.01810.06980.0436-0.0560.10360.02180.01230.1299-0.00830.1187-1.899355.03867.9762
42.01390.9756-2.81762.7714-2.59725.4214-0.47810.9020.5044-1.12850.1434-0.4354-0.48280.55310.08780.4577-0.07720.05910.4637-0.01770.34053.39257.353346.1061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 808 through 855 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 856 through 954 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 955 through 992 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 993 through 1008 )A0

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