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- PDB-1dj3: STRUCTURES OF ADENYLOSUCCINATE SYNTHETASE FROM TRITICUM AESTIVUM ... -

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Basic information

Entry
Database: PDB / ID: 1dj3
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 / IMP metabolic process / 'de novo' AMP biosynthetic process / chloroplast / GTP binding / metal ion binding / cytoplasm
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 speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)96,4734
Polymers95,5862
Non-polymers8862
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-30 kcal/mol
Surface area31150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.44, 151.44, 91.94
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ADENYLOSUCCINATE SYNTHETASE


Mass: 47793.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Cellular location (production host): CYTOSOL / Production host: Escherichia coli (E. coli) / References: UniProt: O24396, 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, lithium sulfate, citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
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
525 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 11, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→33 Å / Num. all: 20426 / Num. obs: 20426 / % possible obs: 84.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.4
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.338 / % possible all: 98.4
Reflection
*PLUS

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 3→10 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh and Huber / Details: NCS restraints were set.
RfactorNum. reflectionSelection details
Rfree0.303 905 random
Rwork0.24 --
all0.24 20426 -
obs0.24 18544 -
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 0 56 0 6636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.139
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.24 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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