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- PDB-1ade: STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE PH 7 AT 25 DEGREES CELSIUS -

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Basic information

Entry
Database: PDB / ID: 1ade
TitleSTRUCTURE OF ADENYLOSUCCINATE SYNTHETASE PH 7 AT 25 DEGREES CELSIUS
ComponentsADENYLOSUCCINATE SYNTHETASE
KeywordsLIGASE (SYNTHETASE) / PURINE NUCLEOTIDE BIOSYNTHESIS / LIGASE / GTP-HYDROLYZING ENZYMES
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; 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
Adenylosuccinate synthetase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 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
Authors: Poland, B.W. / Silva, M.M. / Serra, M.A. / Cho, Y. / Kim, K.H. / Harris, E.M.S. / Honzatko, R.B.
History
DepositionSep 14, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1.4Feb 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

Downloads & links

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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
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-15 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.260, 72.180, 82.900
Angle α, β, γ (deg.)90.00, 108.17, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 236 / 2: CIS PROLINE - PRO B 236
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.54489, -0.21018, -0.81174), (-0.1991, -0.97282, 0.11824), (-0.81453, 0.09719, -0.57192)
Vector: 6.425, 14.55, 8.127)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 1 .. B 431 A 1 .. A 431 1.374

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Components

#1: Protein ADENYLOSUCCINATE SYNTHETASE


Mass: 47269.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: COLI GENETIC STOCK CENTER, STRAIN NUMBER 5408. GIFT FROM DR. B. BACHMAN, GENETIC CENTER, YALE UNIVERSITY
Source: (natural) Escherichia coli (E. coli) / Strain: PUR A STRAIN H1238 / References: UniProt: P0A7D4, adenylosuccinate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTURN TURN_ID: T4, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS, MINUS 45 ...TURN TURN_ID: T4, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS, MINUS 45 DEGREE FROM THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). TURN_ID: T10, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS, MINUS 45 DEGREE FROM THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). TURN_ID: T16, TYPE VIII (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS,MINUS 45 DEGREE FROM THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). TURN_ID: T28, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS, MINUS 45 DEGREE FROM THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). TURN_ID: T29, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS, MINUS 45 DEGREE FROM THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). TURN_ID: T4, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS, MINUS 45 DEGREE FROM THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). TURN_ID: T10, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS, MINUS 45 DEGREE FROM THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). TURN_ID: T16, TYPE VIII (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS,MINUS 45 DEGREE FROM THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). TURN_ID: T28, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS, MINUS 45 DEGREE FROM THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)). TURN_ID: T29, TYPE I (ONE OR MORE OF THE PHI, PSI ANGLES DEVIATE BY MORE THAN PLUS, MINUS 45 DEGREE FROM THE IDEAL VALUES USED BY WILMOT & THORNTON(1989)).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 20-25 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein 1drop
224 %(w/w)PEG33501drop
3100 mMimidazole1drop
5PEG33501reservoir
41reservoirNaCl

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418 Å
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 32567 / % possible obs: 98 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.068
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 54490 / Num. measured all: 174373 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 95 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→5 Å /
RfactorNum. reflection
Rwork0.199 -
obs0.199 174373
Displacement parametersBiso mean: 27 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8266 0 0 1722 9988
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.47
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
Refinement
*PLUS
Num. reflection obs: 49130
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47

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