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- PDB-1kut: Structural Genomics, Protein TM1243, (SAICAR synthetase) -

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Basic information

Entry
Database: PDB / ID: 1kut
TitleStructural Genomics, Protein TM1243, (SAICAR synthetase)
ComponentsPhosphoribosylaminoimidazole-succinocarboxamide synthase
KeywordsSTRUCTURAL GENOMICS / LIGASE / SAICAR synthetase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / cobalamin biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / cytosol
Similarity search - Function
Bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide synthase / SAICAR synthetase signature 1. / SAICAR synthetase, conserved site / SAICAR synthetase/ADE2, N-terminal / SAICAR synthetase / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZhang, R. / Skarina, T. / Beasley, S. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Structure of SAICAR synthase from Thermotoga maritima at 2.2 angstroms reveals an unusual covalent dimer.
Authors: Zhang, R. / Skarina, T. / Evdokimova, E. / Edwards, A. / Savchenko, A. / Laskowski, R. / Cuff, M.E. / Joachimiak, A.
History
DepositionJan 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole-succinocarboxamide synthase
B: Phosphoribosylaminoimidazole-succinocarboxamide synthase


Theoretical massNumber of molelcules
Total (without water)53,0162
Polymers53,0162
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-16 kcal/mol
Surface area22310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.509, 43.067, 80.217
Angle α, β, γ (deg.)90.00, 92.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsProtein TM86 existed in dimer. Chain A and Chain B represent two molecules in the dimer

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Components

#1: Protein Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase


Mass: 26508.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1243 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9X0X0, phosphoribosylaminoimidazolesuccinocarboxamide synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, MgCl2, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 294 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 %PEG40001reservoir
20.15 M1reservoirMgCl2
30.1 MTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793,0.9791,0.95200
DetectorType: SBC-2 / Detector: CCD / Date: Sep 10, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97911
30.9521
ReflectionResolution: 2.14→50 Å / Num. all: 23684 / Num. obs: 23637 / % possible obs: 99.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 6.28 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 20.6
Reflection shellResolution: 2.14→2.25 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.74 / Num. unique all: 3378 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å

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Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→10 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 316887.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: hlml refinement target of CNS was used in the refinement. The number of reflections used in refinement include Friedel pairs. Therefore, the number of reflections for refinement is larger ...Details: hlml refinement target of CNS was used in the refinement. The number of reflections used in refinement include Friedel pairs. Therefore, the number of reflections for refinement is larger than the number collected.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1664 4.8 %RANDOM
Rwork0.245 ---
all-42710 --
obs-35023 82 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.8597 Å2 / ksol: 0.497007 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å20 Å2-2.46 Å2
2--1.44 Å20 Å2
3----5.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 0 81 3583
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 223 5 %
Rwork0.272 4209 -
obs--61.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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