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- PDB-1adi: STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE AT PH 6.5 AND 25 DEGREES... -

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Basic information

Entry
Database: PDB / ID: 1adi
TitleSTRUCTURE OF ADENYLOSUCCINATE SYNTHETASE AT PH 6.5 AND 25 DEGREES CELSIUS
ComponentsADENYLOSUCCINATE SYNTHETASEAdenylosuccinate synthase
KeywordsLIGASE / PURINE NUCLEOTIDE BIOSYNTHESIS / GTP-HYDROLYZING ENZYME
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / 'de novo' AMP biosynthetic process / nucleobase-containing small molecule interconversion / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding ...adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / 'de novo' AMP biosynthetic process / nucleobase-containing small molecule interconversion / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding / magnesium ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, 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 synthase, active site / Adenylosuccinate synthetase active site. / Adenylosuccinate synthase, GTP-binding site / Adenylosuccinate synthetase, domain 2 ...Adenylosuccinate Synthetase, subunit A; domain 2 / Adenylosuccinate Synthetase, subunit A, 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 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
Adenylosuccinate synthetase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSilva, M.M. / Poland, B.W. / Hoffman, C.M. / Fromm, H.J. / Honzatko, R.B.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Refined crystal structures of unligated adenylosuccinate synthetase from Escherichia coli.
Authors: Silva, M.M. / Poland, B.W. / Hoffman, C.R. / Fromm, H.J. / Honzatko, R.B.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Crystal Structure of Adenylosuccinate Synthetase from Escherichia Coli. Evidence for Convergent Evolution of GTP-Binding Domains
Authors: Poland, B.W. / Silva, M.M. / Serra, M.A. / Cho, Y. / Kim, K.H. / Harris, E.M. / Honzatko, R.B.
History
DepositionSep 14, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADENYLOSUCCINATE SYNTHETASE
B: ADENYLOSUCCINATE SYNTHETASE


Theoretical massNumber of molelcules
Total (without water)94,5392
Polymers94,5392
Non-polymers00
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-15 kcal/mol
Surface area32950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.420, 93.630, 119.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.98902, 0.01348, -0.14717), (-0.0386, -0.98482, 0.16923), (-0.14266, 0.17305, 0.97453)
Vector: 31.84475, 89.01199, -5.32704)

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Components

#1: Protein ADENYLOSUCCINATE SYNTHETASE / Adenylosuccinate synthase


Mass: 47269.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
Strain: PUR A STRAIN H1238 (A GIFT FROM DR. B. BACHMAN (GENETIC CENTER, YALE UNIVERSITY))
References: UniProt: P0A7D4, adenylosuccinate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %(w/w)PEG33501reservoir
2100 mMacetic-acid/sodium acetate1reservoir
3200 mMammonium acetate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 104085 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Num. obs: 32170 / Num. measured all: 104085

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Processing

Software
NameClassification
X-PLORrefinement
XENGENdata reduction
RefinementResolution: 2.5→5 Å / σ(F): 0
Details: THERE ARE TWO REGIONS THAT ARE DISORDERED CONSISTING OF RESIDUES 121 - 130 AND 298 - 303.
RfactorNum. reflection
Rwork0.206 -
obs0.206 27502
Displacement parametersBiso mean: 25.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9584 0 0 1317 10901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: 'X-PLOR' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.64

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