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- PDB-3d54: Structure of PurLQS from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 3d54
TitleStructure of PurLQS from Thermotoga maritima
Components
  • Formylglycinamide ribonucleotide amidotransferase
  • Phosphoribosylformylglycinamidine synthase 1
  • Phosphoribosylformylglycinamidine synthase II
KeywordsLIGASE / alpha-beta structure / ATP-binding / Nucleotide-binding / Purine biosynthesis / Glutamine amidotransferase / LIGASE-UNKNOWN FUNCTION COMPLEX
Function / homology
Function and homology information


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / glutaminase / glutaminase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / glutamine metabolic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosylformylglycinamidine synthase subunit PurQ / Formylglycinamide ribonucleotide amidotransferase, C-terminal domain / Phosphoribosylformylglycinamidine subunit PurL, C-terminal / PurL, C-terminal domain superfamily / Phosphoribosylformylglycinamidine synthase II C-terminus / Phosphoribosylformylglycinamidine subunit PurL / Mth169; Chain: A , / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine (FGAM) synthase ...Phosphoribosylformylglycinamidine synthase subunit PurQ / Formylglycinamide ribonucleotide amidotransferase, C-terminal domain / Phosphoribosylformylglycinamidine subunit PurL, C-terminal / PurL, C-terminal domain superfamily / Phosphoribosylformylglycinamidine synthase II C-terminus / Phosphoribosylformylglycinamidine subunit PurL / Mth169; Chain: A , / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine (FGAM) synthase / CobB/CobQ-like glutamine amidotransferase domain / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily / Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / 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 / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Plaits / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine synthase subunit PurQ / Phosphoribosylformylglycinamidine synthase subunit PurL
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsEalick, S.E. / Morar, M.
CitationJournal: Biochemistry / Year: 2008
Title: Formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima: structural insights into complex formation.
Authors: Morar, M. / Hoskins, A.A. / Stubbe, J. / Ealick, S.E.
History
DepositionMay 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 1, 2017Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine synthase II
B: Formylglycinamide ribonucleotide amidotransferase
C: Formylglycinamide ribonucleotide amidotransferase
D: Phosphoribosylformylglycinamidine synthase 1
E: Phosphoribosylformylglycinamidine synthase II
F: Formylglycinamide ribonucleotide amidotransferase
G: Formylglycinamide ribonucleotide amidotransferase
H: Phosphoribosylformylglycinamidine synthase 1
I: Phosphoribosylformylglycinamidine synthase II
J: Formylglycinamide ribonucleotide amidotransferase
K: Formylglycinamide ribonucleotide amidotransferase
L: Phosphoribosylformylglycinamidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,85318
Polymers336,50312
Non-polymers1,3516
Water0
1
I: Phosphoribosylformylglycinamidine synthase II
J: Formylglycinamide ribonucleotide amidotransferase
K: Formylglycinamide ribonucleotide amidotransferase
L: Phosphoribosylformylglycinamidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6186
Polymers112,1684
Non-polymers4502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-47 kcal/mol
Surface area36880 Å2
MethodPISA
2
E: Phosphoribosylformylglycinamidine synthase II
F: Formylglycinamide ribonucleotide amidotransferase
G: Formylglycinamide ribonucleotide amidotransferase
H: Phosphoribosylformylglycinamidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6186
Polymers112,1684
Non-polymers4502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-49 kcal/mol
Surface area36960 Å2
MethodPISA
3
A: Phosphoribosylformylglycinamidine synthase II
B: Formylglycinamide ribonucleotide amidotransferase
C: Formylglycinamide ribonucleotide amidotransferase
D: Phosphoribosylformylglycinamidine synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6186
Polymers112,1684
Non-polymers4502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-46 kcal/mol
Surface area36950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.851, 187.337, 159.177
Angle α, β, γ (deg.)90.00, 99.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphoribosylformylglycinamidine synthase II / / FGAM synthase II


Mass: 69108.961 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: purL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0X3, phosphoribosylformylglycinamidine synthase
#2: Protein
Formylglycinamide ribonucleotide amidotransferase


Mass: 9656.207 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0X1, phosphoribosylformylglycinamidine synthase
#3: Protein Phosphoribosylformylglycinamidine synthase 1 / / Phosphoribosylformylglycinamidine synthase I / FGAM synthase I


Mass: 23746.238 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: purQ / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0X2, phosphoribosylformylglycinamidine synthase
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 5.62 Å3/Da / Density % sol: 78.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 55% MPD, 0.1M HEPES, 7% xylitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.5→45.7 Å / Num. all: 93673 / Num. obs: 78498 / % possible obs: 83.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.5→3.72 Å / % possible all: 66.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→45.7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 127056.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: BULK SOLVENT MODEL USED. THE IDENTITY OF THE METAL ION PRESENT IN THE TMPURLQS STRUCTURE IS UNCERTAIN
RfactorNum. reflection% reflectionSelection details
Rfree0.282 7909 10.1 %RANDOM
Rwork0.252 ---
obs0.252 78498 83.8 %-
all-93673 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.21 Å2 / ksol: 0.25 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.66 Å0.61 Å
Luzzati d res low-5 Å
Luzzati sigma a1.15 Å1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22500 0 84 0 22584
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.454 1003 9.6 %
Rwork0.443 9420 -
obs--66.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1TEMP3.PARAMTEMP3.TOP
X-RAY DIFFRACTION2ADP.PARAMADP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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