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- PDB-1jkx: Unexpected formation of an epoxide-derived multisubstrate adduct ... -

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Basic information

Entry
Database: PDB / ID: 1jkx
TitleUnexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase
ComponentsPHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
KeywordsTRANSFERASE / PURINE BIOSYNTHESIS / ANTI-CANCER AGENT / ENZYME-ASSEMBLED MULTISUBSTRATE ADDUCT INHIBITOR COMPLEX
Function / homology
Function and homology information


phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / DNA damage response / cytoplasm / cytosol
Similarity search - Function
Phosphoribosylglycinamide formyltransferase / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-138 / Phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGreasley, S.E. / Marsilje, T.H. / Cai, H. / Baker, S. / Benkovic, S.J. / Boger, D.L. / Wilson, I.A.
Citation
Journal: Biochemistry / Year: 2001
Title: Unexpected formation of an epoxide-derived multisubstrate adduct inhibitor on the active site of GAR transformylase.
Authors: Greasley, S.E. / Marsilje, T.H. / Cai, H. / Baker, S. / Benkovic, S.J. / Boger, D.L. / Wilson, I.A.
#1: Journal: Bioorg.Med.Chem. / Year: 1997
Title: Functionalized analogues of 5,8,10-trideazafolate: Development of an enzyme-assembled tight binding inhibitor of GAR Tfase and a potential irreversible inhibitor of AICAR Tfase
Authors: Boger, D.L. / Haynes, N.-E. / Warren, M.S. / Ramcharan, J. / Kitos, P.A. / Benkovic, S.J.
History
DepositionJul 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4May 30, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
B: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
C: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
D: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0758
Polymers93,0654
Non-polymers3,0104
Water10,935607
1
A: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
B: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0384
Polymers46,5332
Non-polymers1,5052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
hetero molecules

C: PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0384
Polymers46,5332
Non-polymers1,5052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Unit cell
Length a, b, c (Å)55.140, 56.010, 76.130
Angle α, β, γ (deg.)80.83, 71.71, 83.69
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein
PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE / E.C.2.1.2.2 / Glycinamide Ribonucleotide Transformylase / GART / GAR TRANSFORMYLASE / 5'- ...Glycinamide Ribonucleotide Transformylase / GART / GAR TRANSFORMYLASE / 5'-PHOSPHORIBOSYLGLYCINAMIDE TRANSFORMYLASE


Mass: 23266.254 Da / Num. of mol.: 4 / Fragment: TRANSFERASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURN / Plasmid: PJS167 / Production host: Escherichia coli (E. coli)
References: UniProt: P08179, phosphoribosylglycinamide formyltransferase 1
#2: Chemical
ChemComp-138 / N-[5'-O-PHOSPHONO-RIBOFURANOSYL]-2-[2-HYDROXY-2-[4-[GLUTAMIC ACID]-N-CARBONYLPHENYL]-3-[2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL]-PROPANYLAMINO]-ACETAMIDE


Mass: 752.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H37N6O15P
Details: MAI derived from beta-GAR and the epoxide derivative of 10-bromo-10-bromomethyl-5,8,10-trideazafolic acid
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: PEG 3350, CaCl2, MPD, imidazole malate, PH 7.4, VAPOR DIFFUSION, SITTING DROP at 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
214 %PEG33501reservoir
30.15 M1reservoirCaCl2
44 %MPD1reservoir
50.1 Mimidazole/malate1reservoirpH7.4

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 1998 / Details: MIRRORS
RadiationMonochromator: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 106828 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 6.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6398 / % possible all: 76.4
Reflection
*PLUS
Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 76.4 % / Num. unique obs: 6398

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Processing

Software
NameVersionClassification
EPMRphasing
CNS1refinement
MAR345data collection
MOSFLMdata reduction
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 1C2T

1c2t


Resolution: 1.6→30 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 809232.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.243 10690 10 %RANDOM
Rwork0.221 ---
obs0.221 106744 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1431 Å2 / ksol: 0.355482 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0.47 Å22.66 Å2
2---4.03 Å2-1.77 Å2
3---3.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 208 607 7283
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 1684 10.1 %
Rwork0.299 15040 -
obs--89.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3SOH.PARAMSOH.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scangle_it2.622.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.299

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