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- PDB-3ugj: Formyl Glycinamide ribonucletide amidotransferase from Salmonella... -

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Basic information

Entry
Database: PDB / ID: 3ugj
TitleFormyl Glycinamide ribonucletide amidotransferase from Salmonella Typhimurum: Role of the ATP complexation and glutaminase domain in catalytic coupling
ComponentsPhosphoribosylformylglycinamidine synthase
KeywordsLIGASE / Amidotransferase / Glutaminase / Thioester intermediate
Function / homology
Function and homology information


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / glutamine metabolic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Phosphoribosylformylglycinamidine synthase, linker domain / Phosphoribosylformylglycinamidine synthase PurL / Phosphoribosylformylglycinamidine synthase, N-terminal / Formylglycinamide ribonucleotide amidotransferase N-terminal / FGAR-AT PurM_N-like domain / CobB/CobQ-like glutamine amidotransferase domain / CobB/CobQ-like glutamine amidotransferase domain / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily ...Phosphoribosylformylglycinamidine synthase, linker domain / Phosphoribosylformylglycinamidine synthase PurL / Phosphoribosylformylglycinamidine synthase, N-terminal / Formylglycinamide ribonucleotide amidotransferase N-terminal / FGAR-AT PurM_N-like domain / CobB/CobQ-like glutamine amidotransferase domain / CobB/CobQ-like glutamine amidotransferase domain / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Phosphoribosylformylglycinamidine synthase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsMorar, M. / Tanwar, A.S. / Panjikar, S. / Anand, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Formylglycinamide ribonucleotide amidotransferase from Salmonella typhimurium: role of ATP complexation and the glutaminase domain in catalytic coupling
Authors: Tanwar, A.S. / Morar, M. / Panjikar, S. / Anand, R.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Phosphoribosylformylglycinamidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,41810
Polymers142,4371
Non-polymers9809
Water14,772820
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)145.983, 145.983, 141.149
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Phosphoribosylformylglycinamidine synthase / FGAM synthase / FGAMS / Formylglycinamide ribotide amidotransferase / FGARAT / Formylglycinamide ...FGAM synthase / FGAMS / Formylglycinamide ribotide amidotransferase / FGARAT / Formylglycinamide ribotide synthetase


Mass: 142437.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
References: UniProt: P74881, phosphoribosylformylglycinamidine synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 3.05 Å3/Da / Density % sol: 59.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 2M Ammonium Sulphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.78→30 Å / Num. obs: 15661 / % possible obs: 99.2 %
Reflection shellHighest resolution: 1.78 Å / Redundancy: 3.7 % / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.24 -Random
Rwork0.2109 --
obs-15661 -
Displacement parametersBiso max: 139.56 Å2 / Biso mean: 16.4144 Å2 / Biso min: 1 Å2
Refinement stepCycle: LAST / Resolution: 1.78→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9884 0 55 820 10759
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.36

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