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- PDB-1dj2: STRUCTURES OF ADENYLOSUCCINATE SYNTHETASE FROM TRITICUM AESTIVUM ... -

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Basic information

Entry
Database: PDB / ID: 1dj2
TitleSTRUCTURES OF ADENYLOSUCCINATE SYNTHETASE FROM TRITICUM AESTIVUM AND ARABIDOPSIS THALIANA
ComponentsADENYLOSUCCINATE SYNTHETASE
KeywordsLIGASE / GDP
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / 'de novo' AMP biosynthetic process / apoplast / chloroplast stroma / plastid / chloroplast / GTP binding / magnesium ion binding
Similarity search - Function
Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 ...Adenylosuccinate Synthetase; Chain A, domain 1 / Adenylosuccinate Synthetase, subunit A, domain 1 / Adenylosuccinate Synthetase; Chain A, domain 3 / Adenylosuccinate Synthetase, subunit A, domain 3 / Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, domain 2 / Adenylosuccinate synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, domain 1 / Adenylosuccinate synthetase / Adenylosuccinate synthetase / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Adenylosuccinate synthetase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsPrade, L. / Cowan-Jacob, S.W. / Chemla, P. / Potter, S. / Ward, E. / Fonne-Pfister, R.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structures of adenylosuccinate synthetase from Triticum aestivum and Arabidopsis thaliana.
Authors: Prade, L. / Cowan-Jacob, S.W. / Chemla, P. / Potter, S. / Ward, E. / Fonne-Pfister, R.
History
DepositionDec 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENYLOSUCCINATE SYNTHETASE
B: ADENYLOSUCCINATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6594
Polymers95,7732
Non-polymers8862
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-26 kcal/mol
Surface area30680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.76, 212.76, 212.76
Angle α, β, γ (deg.)90, 90, 90
Int Tables number197
Space group name H-MI23

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Components

#1: Protein ADENYLOSUCCINATE SYNTHETASE


Mass: 47886.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Cellular location (production host): CYTOSOL / Production host: Escherichia coli (E. coli) / References: UniProt: Q96529, adenylosuccinate synthase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, 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: 4.19 Å3/Da / Density % sol: 70.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 4000, Lithium sulfate, citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
210 mMHEPES1drop
30.1 Msodium citrate1reservoir
40.2 M1reservoirLi2SO4
523 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 28, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→45 Å / Num. all: 33374 / Num. obs: 33374 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.433 / % possible all: 87.9
Reflection
*PLUS

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.9→45 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 1850 RANDOM
Rwork0.233 --
all0.233 33374 -
obs0.233 27208 -
Refinement stepCycle: LAST / Resolution: 2.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6556 0 56 0 6612
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.122
X-RAY DIFFRACTIONx_bond_d0.005
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 45 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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