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- PDB-4zz0: Human GAR transformylase in complex with GAR and (S)-2-(8-(2-Amin... -

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Basic information

Entry
Database: PDB / ID: 4zz0
TitleHuman GAR transformylase in complex with GAR and (S)-2-(8-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)octanamido)pentanedioic acid (AGF147)
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-3YE / GLYCINAMIDE RIBONUCLEOTIDE / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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)23,5163
Polymers22,8101
Non-polymers7062
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.240, 75.240, 100.409
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-3YE / (S)-2-(8-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)octanamido)pentanedioic acid


Mass: 421.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H27N5O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.83 Å3/Da / Density % sol: 67.91 %
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: 1.65→50 Å / Num. obs: 40099 / % possible obs: 99.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 13.73 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.025 / Rrim(I) all: 0.081 / Χ2: 1.008 / Net I/av σ(I): 28.12 / Net I/σ(I): 17.2 / Num. measured all: 387613
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.686.20.45319330.8740.1860.4920.57897.7
1.68-1.717.30.39219700.9270.150.4210.60399.8
1.71-1.748.20.3719850.9520.1350.3940.63899.9
1.74-1.788.90.31819580.9610.1120.3370.706100
1.78-1.829.40.29719940.9740.1010.3140.82100
1.82-1.869.60.23919880.9840.0810.2530.884100
1.86-1.99.80.19519780.9890.0650.2060.819100
1.9-1.969.90.16619920.9930.0550.1750.962100
1.96-2.019.90.14719850.9930.0490.1540.995100
2.01-2.08100.12520040.9950.0410.1321.138100
2.08-2.1510.10.10419820.9960.0340.111.057100
2.15-2.2410.20.09620020.9950.0310.1011.051100
2.24-2.3410.20.09319960.9960.030.0981.163100
2.34-2.4610.30.08520120.9960.0280.091.129100
2.46-2.6210.40.08120340.9960.0260.0851.169100
2.62-2.8210.50.07820040.9970.0250.0831.261100
2.82-3.1110.60.07420310.9970.0240.0771.346100
3.11-3.5510.60.06520360.9980.0210.0681.243100
3.55-4.4810.60.0620660.9970.0190.0631.124100
4.48-5010.20.05621490.9980.0180.0590.91398.5

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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: 4X78

4x78
PDB Unreleased entry


Resolution: 1.65→39.769 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1852 1998 5.04 %
Rwork0.1598 37663 -
obs0.1611 39661 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.37 Å2 / Biso mean: 20.3105 Å2 / Biso min: 5.45 Å2
Refinement stepCycle: final / Resolution: 1.65→39.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 48 196 1747
Biso mean--34.39 26.61 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061720
X-RAY DIFFRACTIONf_angle_d1.1532354
X-RAY DIFFRACTIONf_chiral_restr0.049272
X-RAY DIFFRACTIONf_plane_restr0.006311
X-RAY DIFFRACTIONf_dihedral_angle_d13.614645
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 (%)
1.6489-1.69010.2311250.21492223234883
1.6901-1.73580.21671380.19372656279499
1.7358-1.78690.17871440.173927222866100
1.7869-1.84460.18911380.167926892827100
1.8446-1.91050.19061440.158726682812100
1.9105-1.9870.18361410.165927162857100
1.987-2.07740.19591430.16326912834100
2.0774-2.18690.15561450.151427232868100
2.1869-2.32390.1571430.151827172860100
2.3239-2.50330.21791470.163327442891100
2.5033-2.75520.2021390.174427052844100
2.7552-3.15370.20641520.173127692921100
3.1537-3.97280.16691460.149327732919100
3.9728-39.78080.17431530.13842867302099
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)
11.4588-0.115-0.98310.81040.75143.35430.10430.07070.1275-0.2069-0.0529-0.0039-0.3609-0.1194-0.05650.15060.00870.0110.0633-0.01920.0926-41.675323.2051-24.3986
22.91851.3363-1.40441.1875-1.21414.1361-0.03880.17850.4561-0.49050.14850.0859-0.61150.0614-0.14480.3565-0.0320.04120.0989-0.00220.2179-35.804930.6708-29.9935
31.1624-0.51320.52820.9320.39060.8407-0.02560.24740.5237-0.48560.153-0.486-0.7810.7915-0.07880.3056-0.31080.17380.2328-0.13880.3696-23.381430.8232-25.001
40.5535-0.1855-0.28561.13070.8531.05850.0421-0.11860.1172-0.03410.1791-0.2582-0.09430.3063-0.16580.0868-0.03110.01140.1478-0.04330.1285-27.611613.4877-28.0898
50.7655-0.2501-0.64460.76330.21873.3280.01260.02430.0717-0.0410.0567-0.0014-0.0297-0.0087-0.04240.0511-0.0096-0.00020.049-0.00320.0692-39.500710.106-34.4658
67.4829-2.14640.30872.4844-0.07533.7827-0.358-0.543-0.36260.70570.1273-0.49320.49770.71920.1520.23820.0776-0.01790.26830.01740.2093-34.04897.979-12.6536
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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