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- PDB-2gqr: SAICAR Synthetase Complexed with ADP-Mg2+ -

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Basic information

Entry
Database: PDB / ID: 2gqr
TitleSAICAR Synthetase Complexed with ADP-Mg2+
ComponentsPhosphoribosylaminoimidazole-succinocarboxamide synthase
KeywordsLIGASE / PurC / Ade2 / Ade1 / nucleotide complex / octahedral magnesium coordination / alternate folding
Function / homology
Function and homology information


phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / cobalamin biosynthetic process / 'de novo' IMP biosynthetic process / guanosine tetraphosphate binding / ATP binding / membrane / cytosol
Similarity search - Function
Bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide synthase / Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / 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 ...Bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide synthase / Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase signature 1. / SAICAR synthetase signature 2. / 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
ADENOSINE-5'-DIPHOSPHATE / Phosphoribosylaminoimidazole-succinocarboxamide synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsGinder, N.D. / Honzatko, R.B.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Nucleotide Complexes of Escherichia coli Phosphoribosylaminoimidazole Succinocarboxamide Synthetase.
Authors: Ginder, N.D. / Binkowski, D.J. / Fromm, H.J. / Honzatko, R.B.
History
DepositionApr 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8076
Polymers54,9042
Non-polymers9034
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-47 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.290, 67.160, 148.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer with 2-fold symmetry wholly contained within the asymmetric unit.

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Components

#1: Protein Phosphoribosylaminoimidazole-succinocarboxamide synthase / SAICAR synthetase


Mass: 27452.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: purC / Production host: Escherichia coli (E. coli)
References: UniProt: P0A7D7, phosphoribosylaminoimidazolesuccinocarboxamide synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Well Solution: 3.4-3.8 M sodium formate, 50 mM Tris; Protein Solution: 15 mg/mL Protein, 50 mM ADP, 5 mM DTT, 5 mM EDTA, 15 mM Tris, 25 mM KCl, 55 mM magnesium chloride , pH 8.5, VAPOR ...Details: Well Solution: 3.4-3.8 M sodium formate, 50 mM Tris; Protein Solution: 15 mg/mL Protein, 50 mM ADP, 5 mM DTT, 5 mM EDTA, 15 mM Tris, 25 mM KCl, 55 mM magnesium chloride , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97900, 0.97884, 0.98671
DetectorType: NOIR-1 / Detector: CCD
RadiationMonochromator: Double Crystal-Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.978841
30.986711
ReflectionResolution: 2→46.39 Å / Num. all: 40775 / Num. obs: 40775 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.02 % / Rmerge(I) obs: 0.067 / Χ2: 0.97 / Net I/σ(I): 16.3 / Scaling rejects: 2163
Reflection shellResolution: 2→2.07 Å / % possible obs: 95.8 % / Redundancy: 5.42 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.7 / Num. measured all: 21027 / Num. unique obs: 3842 / Χ2: 1.26 / % possible all: 95.8

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Processing

Software
NameVersionClassificationNB
d*TREK9.2LDzdata processing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
d*TREKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→24.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1729656.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4089 10 %RANDOM
Rwork0.204 ---
all0.208 40702 --
obs0.208 40702 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.576 Å2 / ksol: 0.398 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---2.97 Å20 Å2
3---2.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3788 0 56 363 4207
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d3.55
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.542
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 670 10.3 %
Rwork0.226 5818 -
obs-6488 96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION5carbohydrate.param

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