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- PDB-3ujn: Formyl Glycinamide Ribonucleotide Amidotransferase from Salmonell... -

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Basic information

Entry
Database: PDB / ID: 3ujn
TitleFormyl Glycinamide Ribonucleotide Amidotransferase from Salmonella Typhimurium : Role of the ATP complexation and glutaminase domain in catalytic coupling
ComponentsPhosphoribosylformylglycinamidine synthase
KeywordsLIGASE / Amidotransferase / Glutaminase
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 / 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 ...Phosphoribosylformylglycinamidine synthase, linker domain / Phosphoribosylformylglycinamidine synthase PurL / Phosphoribosylformylglycinamidine synthase, N-terminal / Formylglycinamide ribonucleotide amidotransferase N-terminal / 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: 2.98 Å
AuthorsAnand, R. / Morar, M. / Tanwar, A.S. / Panjikar, S.
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 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2597
Polymers142,5661
Non-polymers6926
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)146.958, 146.958, 141.2
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: 142566.406 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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 / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
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: ESRF / Beamline: BM14 / Wavelength: 0.817 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.817 Å / Relative weight: 1
ReflectionResolution: 2.98→20 Å / Num. obs: 69080 / Observed criterion σ(F): 0
Reflection shellHighest resolution: 2.98 Å / Redundancy: 2.9 % / Num. unique all: 34973

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2643 3470 random
Rwork0.2083 --
all-34973 -
obs-31503 -
Displacement parametersBiso max: 88.73 Å2 / Biso mean: 27.806 Å2 / Biso min: 1 Å2
Refinement stepCycle: LAST / Resolution: 2.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9910 0 40 255 10205
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellHighest resolution: 2.98 Å
RfactorNum. reflection
Rfree0.2643 3470
Rwork0.2083 -
obs-31503

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