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- PDB-1j4b: Recombinant Mouse-Muscle Adenylosuccinate Synthetase -

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Basic information

Entry
Database: PDB / ID: 1j4b
TitleRecombinant Mouse-Muscle Adenylosuccinate Synthetase
Componentsadenylosuccinate synthetase
KeywordsLIGASE / GTP-hydrolyzing enzymes / purine nucleotide cycle
Function / homology
Function and homology information


Purine ribonucleoside monophosphate biosynthesis / purine nucleotide metabolic process / adenylosuccinate synthase / adenylosuccinate synthase activity / aspartate metabolic process / cellular response to electrical stimulus / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / glutamine metabolic process ...Purine ribonucleoside monophosphate biosynthesis / purine nucleotide metabolic process / adenylosuccinate synthase / adenylosuccinate synthase activity / aspartate metabolic process / cellular response to electrical stimulus / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / glutamine metabolic process / response to starvation / response to muscle activity / cellular response to xenobiotic stimulus / actin filament binding / GTPase activity / GTP binding / magnesium ion binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
Adenylosuccinate synthetase isozyme 1, chordates / 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 isozyme 1, chordates / 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 isozyme 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIancu, C.V. / Borza, T. / Choe, J.Y. / Fromm, H.J. / Honzatko, R.B.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Recombinant mouse muscle adenylosuccinate synthetase: overexpression, kinetics, and crystal structure.
Authors: Iancu, C.V. / Borza, T. / Choe, J.Y. / Fromm, H.J. / Honzatko, R.B.
History
DepositionSep 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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


Theoretical massNumber of molelcules
Total (without water)50,3211
Polymers50,3211
Non-polymers00
Water1,72996
1
A: adenylosuccinate synthetase

A: adenylosuccinate synthetase


Theoretical massNumber of molelcules
Total (without water)100,6432
Polymers100,6432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5960 Å2
ΔGint-23 kcal/mol
Surface area32360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.930, 69.930, 198.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein adenylosuccinate synthetase / AdSS1


Mass: 50321.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: muscle / Cellular location: cytoplasm / Gene: Adss1 / Plasmid: pET28b / Species (production host): Escherichia coli / Cellular location (production host): cytoplasm / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P28650, adenylosuccinate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.5
Details: Cacodylate 100 mM, pH6.5 PEG 8000 18% 200 mM Calcium Acetate
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMHEPES1droppH7.5
350 mM1dropNaCl
41 mMdithiothreitol1drop
50.5 mMEDTA1drop
6200 mMcalcium acetate1reservoir
7100 mMcacodylate1reservoirpH6.5
818 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→39.6 Å / Num. obs: 16066 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 24
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2 / Rsym value: 0.224 / % possible all: 60
Reflection
*PLUS
Num. measured all: 132963
Reflection shell
*PLUS
% possible obs: 60 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SON

1son


Resolution: 2.5→39.61 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 132841.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1588 9.9 %RANDOM
Rwork0.207 ---
obs0.207 16060 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.0352 Å2 / ksol: 0.357928 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å20 Å2
2--1.96 Å20 Å2
3----3.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→39.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 96 3454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 167 9.3 %
Rwork0.265 1629 -
obs--62.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2LIG.PARAM
X-RAY DIFFRACTION3PARAM19.SOL
X-RAY DIFFRACTION4ION.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.336 / % reflection Rfree: 9.3 % / Rfactor Rwork: 0.265

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