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- PDB-1c3e: NEW INSIGHTS INTO INHIBITOR DESIGN FROM THE CRYSTAL STRUCTURE AND... -

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Basic information

Entry
Database: PDB / ID: 1c3e
TitleNEW INSIGHTS INTO INHIBITOR DESIGN FROM THE CRYSTAL STRUCTURE AND NMR STUDIES OF E. COLI GAR TRANSFORMYLATE IN COMPLEX WITH BETA-GAR AND 10-FORMYL-5,8,10-TRIDEAZAFOLIC ACID.
ComponentsGLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
KeywordsTRANSFERASE / PURINE BIOSYNTHESIS / ANTI-CANCER AGENT / 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
GLYCINAMIDE RIBONUCLEOTIDE / Chem-NHR / Phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsGreasley, S.E. / Yamashita, M.M. / Cai, H. / Benkovic, S.J. / Boger, D.L. / Wilson, I.A.
Citation
Journal: Biochemistry / Year: 1999
Title: New insights into inhibitor design from the crystal structure and NMR studies of Escherichia coli GAR transformylase in complex with beta-GAR and 10-formyl-5,8,10-trideazafolic acid.
Authors: Greasley, S.E. / Yamashita, M.M. / Cai, H. / Benkovic, S.J. / Boger, D.L. / Wilson, I.A.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: A pH Dependent Stabilization of an Active Site Loop Observed from Low and High pH Crystal Structures of Mutant Monomeric Glycinamide Ribonucleotide Transformylase at 1.8-1.9A
Authors: Su, Y. / Yamashita, M.M. / Greasley, S.E. / Mullen, C.A. / Shim, J.H. / Jennings, P.A. / Benkovic, S.J. / Wilson, I.A.
#2: Journal: Bioorg.Med.Chem. / Year: 1997
Title: 10-Formyl-5,8,10-trideazafolic acid (10-formyl-TDAF):a Potent Inhibitor of Glycinamide Ribonucleotide Transformylase.
Authors: Boger, D.L. / Haynes, N.-E. / Kitos, P.A. / Ramcharan, J. / Marolewski, A.E. / Benkovic, S.J.
History
DepositionJul 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: 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
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
B: GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4356
Polymers45,9022
Non-polymers1,5334
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.250, 112.790, 46.960
Angle α, β, γ (deg.)90.00, 101.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE


Mass: 22950.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PURN / Production host: Escherichia coli (E. coli)
References: UniProt: P08179, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-NHR / 2-{4-[2-(2-AMINO-4-HYDROXY-QUINAZOLIN-6-YL)-1-CARBOXY-ETHYL]-BENZOYLAMINO}-PENTANEDIOIC ACID / (10R)-10-FORMYL-5,8,10-TRIDEAZAFOLIC ACID


Mass: 482.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H22N4O8
#3: Chemical ChemComp-GAR / GLYCINAMIDE RIBONUCLEOTIDE


Mass: 284.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 3350, Imidazole malate, calcium chloride, MPD, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 22.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
218 %(v/v)PEG33501reservoir
30.1 Mimidazole/malate1reservoir
40.15 M1reservoirCaCl2
54 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 23742 / Num. obs: 23742 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.421 / Num. unique all: 2338 / % possible all: 99.3
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.3 % / Num. unique obs: 2338 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.3refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 471792.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 917 4.9 %RANDOM
Rwork0.227 ---
obs0.227 18882 78.9 %-
all-23742 --
Displacement parametersBiso mean: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.7 Å20 Å24.3 Å2
2--11.05 Å20 Å2
3----3.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 106 197 3539
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 111 5.1 %
Rwork0.279 2077 -
obs--54.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAGARA.TOP
X-RAY DIFFRACTION3GARA.PARNEH9RH.TOP
X-RAY DIFFRACTION4NEH9RH.PAR
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.304 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.279

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