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- PDB-4ew3: The structure of human glycinamide ribonucleotide transformylase ... -

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Basic information

Entry
Database: PDB / ID: 4ew3
TitleThe structure of human glycinamide ribonucleotide transformylase in complex with 10R-methylthio-DDATHF.
ComponentsTrifunctional purine biosynthetic protein adenosine-3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / phosphoribosylamine-glycine ligase activity / brainstem development / 'de novo' XMP biosynthetic process ...phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / phosphoribosylamine-glycine ligase activity / brainstem development / 'de novo' XMP biosynthetic process / 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
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 / 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 / Phosphoribosylformylglycinamidine cyclo-ligase / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / 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-DXZ / PHOSPHATE ION / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsConnelly, S. / DeMartino, K. / Boger, D.L. / Wilson, I.A.
CitationJournal: Biochemistry / Year: 2013
Title: Biological and Structural Evaluation of 10R- and 10S-Methylthio-DDACTHF Reveals a New Role for Sulfur in Inhibition of Glycinamide Ribonucleotide Transformylase.
Authors: Connelly, S. / Demartino, J.K. / Boger, D.L. / Wilson, I.A.
History
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Trifunctional purine biosynthetic protein adenosine-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4445
Polymers22,6791
Non-polymers7654
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Trifunctional purine biosynthetic protein adenosine-3
hetero molecules

A: Trifunctional purine biosynthetic protein adenosine-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,88710
Polymers45,3582
Non-polymers1,5298
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area1450 Å2
ΔGint-7 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.124, 78.124, 230.048
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

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Components

#1: Protein Trifunctional purine biosynthetic protein adenosine-3 / Phosphoribosylamine--glycine ligase / Glycinamide ribonucleotide synthetase / GARS / ...Phosphoribosylamine--glycine ligase / Glycinamide ribonucleotide synthetase / GARS / Phosphoribosylglycinamide synthetase / Phosphoribosylformylglycinamidine cyclo-ligase / AIR synthase / AIRS / Phosphoribosyl-aminoimidazole synthetase / Phosphoribosylglycinamide formyltransferase / 5'-phosphoribosylglycinamide transformylase / GAR transformylase / GART


Mass: 22678.941 Da / Num. of mol.: 1 / Fragment: 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): Bl21 (DE3) Gold
References: UniProt: P22102, phosphoribosylamine-glycine ligase, phosphoribosylformylglycinamidine cyclo-ligase, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DXZ / N-({4-[(1R)-4-(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)-1-(methylsulfanyl)butyl]phenyl}carbonyl)-L-glutamic acid


Mass: 477.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N5O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 4.47 Å3/Da / Density % sol: 72.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M phosphate/citrate buffer, 1.5-2.0 M ammonium sulfate at p.H 4.2. 25% Glycerol added as , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 5, 2007
Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→67.73 Å / Num. obs: 46588 / % possible obs: 99.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.042 / Net I/σ(I): 38.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 10 % / Mean I/σ(I) obs: 38.3 / Num. unique all: 4512 / Rsym value: 0.696 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MEO

1meo


Resolution: 1.702→67.73 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.86 / SU B: 3.562 / SU ML: 0.052 / SU R Cruickshank DPI: 0.092 / SU Rfree: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2349 5.1 %RANDOM
Rwork0.2 ---
obs0.2 46452 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.27 Å2 / Biso mean: 29.368 Å2 / Biso min: 12.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.18 Å20 Å2
2---0.37 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.702→67.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 48 167 1769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221770
X-RAY DIFFRACTIONr_bond_other_d0.0020.021178
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.982423
X-RAY DIFFRACTIONr_angle_other_deg1.1313.0022895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69125.19577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10815315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7141510
X-RAY DIFFRACTIONr_chiral_restr0.10.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022013
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02328
X-RAY DIFFRACTIONr_mcbond_it1.5681.51101
X-RAY DIFFRACTIONr_mcbond_other1.0741.5445
X-RAY DIFFRACTIONr_mcangle_it2.38521797
X-RAY DIFFRACTIONr_scbond_it3.2293669
X-RAY DIFFRACTIONr_scangle_it4.7844.5616
X-RAY DIFFRACTIONr_rigid_bond_restr1.7132948
X-RAY DIFFRACTIONr_sphericity_free10.5333167
X-RAY DIFFRACTIONr_sphericity_bonded7.21232907
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 172 -
Rwork0.307 3180 -
all-3352 -
obs--99.55 %

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