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- PDB-4zz1: HUMAN GAR TRANSFORMYLASE IN COMPLEX WITH GAR AND (S)-2-({4-[3-(2-... -

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Basic information

Entry
Database: PDB / ID: 4zz1
TitleHUMAN GAR TRANSFORMYLASE IN COMPLEX WITH GAR AND (S)-2-({4-[3-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-6-YL)-PROPYL]-THIOPHENE-2-CARBONYL}-AMINO)-PENTANEDIOIC ACID
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-3YF / GLYCINAMIDE RIBONUCLEOTIDE / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.351 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: J.Med.Chem. / Year: 2015
Title: 6-Substituted Pyrrolo[2,3-d]pyrimidine Thienoyl Regioisomers as Targeted Antifolates for Folate Receptor alpha and the Proton-Coupled Folate Transporter in Human Tumors.
Authors: Wang, L. / Wallace, A. / Raghavan, S. / Deis, S.M. / Wilson, M.R. / Yang, S. / Polin, L. / White, K. / Kushner, J. / Orr, S. / George, C. / O'Connor, C. / Hou, Z. / Mitchell-Ryan, S. / Dann, ...Authors: Wang, L. / Wallace, A. / Raghavan, S. / Deis, S.M. / Wilson, M.R. / Yang, S. / Polin, L. / White, K. / Kushner, J. / Orr, S. / George, C. / O'Connor, C. / Hou, Z. / Mitchell-Ryan, S. / Dann, C.E. / Matherly, L.H. / Gangjee, A.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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

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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
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.344, 75.344, 100.736
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1504-

HOH

21A-1522-

HOH

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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, phosphoribosylamine-glycine ligase, phosphoribosylformylglycinamidine cyclo-ligase, 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-3YF / (S)-2-({4-[3-(2-Amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-6-yl)-propyl]-thiophene-2-carbonyl}-amino)-pentanedioic acid


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


Mass: 18.015 Da / Num. of mol.: 328 / 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: 68.1 %
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: 1.35→50 Å / Num. obs: 71990 / % possible obs: 98.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 13.91 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Χ2: 0.998 / Net I/av σ(I): 27.77 / Net I/σ(I): 18.7 / Num. measured all: 698175
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.373.60.4331770.8460.2310.4910.80988.9
1.37-1.45.20.42435580.9010.1940.4690.75299
1.4-1.437.20.39636110.9350.1560.4260.758100
1.43-1.458.90.35135780.9650.1240.3720.755100
1.45-1.499.90.30935900.980.1040.3260.771100
1.49-1.5210.20.26136230.9820.0860.2750.816100
1.52-1.5610.40.2236220.9880.0720.2320.875100
1.56-1.610.40.19136070.9910.0620.2010.983100
1.6-1.6510.50.15636120.9940.050.1640.867100
1.65-1.710.60.13636170.9950.0440.1430.903100
1.7-1.7610.60.11536190.9960.0370.1210.971100
1.76-1.8310.70.09536470.9970.030.11.032100
1.83-1.9210.70.08336170.9970.0260.0871.021100
1.92-2.0210.80.07636140.9980.0240.081.102100
2.02-2.1410.90.07236690.9980.0230.0761.219100
2.14-2.3110.90.0736350.9970.0220.0731.25100
2.31-2.54110.06936830.9970.0220.0731.306100
2.54-2.91110.06436880.9980.020.0671.243100
2.91-3.6610.50.05837090.9970.0190.0611.12899.5
3.66-508.90.05235140.9960.0190.0550.88190.3

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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: 4X79

4x79
PDB Unreleased entry


Resolution: 1.351→39.871 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 14.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1577 2004 2.86 %
Rwork0.1396 68153 -
obs0.1402 70157 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.41 Å2 / Biso mean: 23.5851 Å2 / Biso min: 7.41 Å2
Refinement stepCycle: final / Resolution: 1.351→39.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 49 328 1880
Biso mean--21.55 37.9 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061695
X-RAY DIFFRACTIONf_angle_d1.1632320
X-RAY DIFFRACTIONf_chiral_restr0.046269
X-RAY DIFFRACTIONf_plane_restr0.006305
X-RAY DIFFRACTIONf_dihedral_angle_d12.53635
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 (%)
1.3508-1.38450.2033850.19762886297158
1.3845-1.4220.17761420.17734822496496
1.422-1.46380.19911480.162349845132100
1.4638-1.51110.18031470.147250105157100
1.5111-1.56510.13581480.138750025150100
1.5651-1.62770.14351500.133150275177100
1.6277-1.70180.16091460.136450175163100
1.7018-1.79150.181470.142550685215100
1.7915-1.90380.16511460.137650275173100
1.9038-2.05080.15381470.134450595206100
2.0508-2.25710.13831490.131650785227100
2.2571-2.58370.16931500.142150985248100
2.5837-3.2550.17471500.142851425292100
3.255-39.88830.14031490.13334933508293
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)
11.2984-0.1424-1.02720.94410.11313.29420.031-0.18450.01950.0326-0.0202-0.07620.00890.3101-0.0090.1028-0.01780.00940.15480.0020.125740.8883-24.5589-26.0697
21.41160.2533-0.58441.45170.71793.68340.1972-0.35590.16920.1955-0.117-0.29-0.30380.5433-0.11620.1846-0.0999-00.2553-0.02420.201844.8294-15.7767-20.3796
31.9214-0.9612-0.64921.91520.40131.72560.1248-0.14360.42730.3368-0.0918-0.1553-0.65590.3049-0.22230.3674-0.12390.07790.1957-0.07340.311640.9903-5.6543-21.9638
42.4594-0.5188-1.64621.99430.14422.62850.3290.08730.5491-0.0088-0.045-0.1165-0.4882-0.1201-0.17560.3676-0.03450.11510.12820.00430.302736.1101-4.4518-29.2893
51.5968-0.4391-1.04191.47290.17432.66250.26360.03020.3286-0.0255-0.05450.0076-0.4685-0.0721-0.19450.2271-0.00190.06080.11160.01090.180932.4511-11.7931-28.4745
61.38370.239-1.25670.6613-0.66442.85270.12810.0580.1760.0043-0.02250.037-0.2505-0.1081-0.14230.12640.00640.00770.09780.00050.12922.5518-19.9265-19.9022
70.89020.2024-0.60610.4062-0.07922.97210.0325-0.06280.02530.0413-0.015-0.04440.04040.06920.04190.0916-0.00250.00220.0719-0.00370.090928.5635-29.0135-15.9966
84.8666-0.26520.52552.568-0.69632.239-0.06590.74080.042-0.3853-0.15470.6168-0.0298-0.8161-0.08910.16260.0371-0.03860.3494-0.02830.202923.1636-25.4408-37.7134
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 870 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 871 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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