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- PDB-3viu: Crystal structure of PurL from thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 3viu
TitleCrystal structure of PurL from thermus thermophilus
ComponentsPhosphoribosylformylglycinamidine synthase 2
KeywordsLIGASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / PURINE METABOLISM / ATP-BINDING
Function / homology
Function and homology information


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / 'de novo' IMP biosynthetic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosylformylglycinamidine subunit PurL / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / 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 ...Phosphoribosylformylglycinamidine subunit PurL / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / 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 / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Phosphoribosylformylglycinamidine synthase subunit PurL
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsSuzuki, S. / Yanai, H. / Kanagawa, M. / Tamura, S. / Watanabe, Y. / Fuse, K. / Baba, S. / Sampei, G. / Kawai, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of N-formylglycinamide ribonucleotide amidotransferase II (PurL) from Thermus thermophilus HB8
Authors: Suzuki, S. / Yanai, H. / Kanagawa, M. / Tamura, S. / Watanabe, Y. / Fuse, K. / Baba, S. / Sampei, G. / Kawai, G.
History
DepositionOct 12, 2011Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 18, 2012ID: 3AC6
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0035
Polymers79,3511
Non-polymers6534
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.899, 94.563, 158.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoribosylformylglycinamidine synthase 2 / / Phosphoribosylformylglycinamidine synthase II / FGAM synthase II


Mass: 79350.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: purL, TTHA1519 / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 834(DE3)
References: UniProt: Q5SMH8, phosphoribosylformylglycinamidine synthase

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Non-polymers , 5 types, 300 molecules

#2: 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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.1
Details: 25% PEG 3350, 0.2M ammonium acetate, 0.1M MES, pH 7.1, VAPOR DIFFUSION, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.979291, 1.0, 0.979541
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 23, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792911
211
30.9795411
ReflectionResolution: 2.35→47.28 Å / Num. all: 30356 / Num. obs: 29532 / % possible obs: 97.3 % / Redundancy: 6.1 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 14
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2993 / % possible all: 78.2

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.35→47.28 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 70314.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2818 10 %RANDOM
Rwork0.199 ---
obs0.199 28300 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.9862 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.12 Å20 Å20 Å2
2--0.32 Å20 Å2
3---4.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.35→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5371 0 40 296 5707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.452
X-RAY DIFFRACTIONc_scangle_it3.522.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 434 11 %
Rwork0.254 3508 -
obs--78.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6adp.paramadp.top
X-RAY DIFFRACTION7peg.parampeg.top

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