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- PDB-1mf1: Structure of the Recombinant Mouse-Muscle Adenylosuccinate Synthe... -

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Basic information

Entry
Database: PDB / ID: 1mf1
TitleStructure of the Recombinant Mouse-Muscle Adenylosuccinate Synthetase Complexed with AMP
ComponentsAdenylosuccinate Synthetase
KeywordsLIGASE / Purine biosynthesis / GTP-binding / Multigene family
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
ACETATE ION / ADENOSINE MONOPHOSPHATE / Adenylosuccinate synthetase isozyme 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsIancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Feedback inhibition and product complexes of recombinant mouse muscle adenylosuccinate synthetase.
Authors: Iancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B.
History
DepositionAug 9, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 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

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Assembly

Deposited unit
A: Adenylosuccinate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7283
Polymers50,3211
Non-polymers4062
Water81145
1
A: Adenylosuccinate Synthetase
hetero molecules

A: Adenylosuccinate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4556
Polymers100,6432
Non-polymers8134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area7510 Å2
ΔGint-30 kcal/mol
Surface area29830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.240, 70.240, 199.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological unit is a dimer. The other monomer is generated by:2-y, 2-x, 1/2-z.

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Components

#1: Protein Adenylosuccinate Synthetase / ADSS / AMPSASE


Mass: 50321.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adss1 / Plasmid: Pet28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P28650, adenylosuccinate synthase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMHEPES1droppH7.
350 mM1dropNaCl
41 mMdithiothreitol1drop
50.5 mMEDTA1drop
610 mMAMP1drop
710 mMmagnesium acetate1drop
8100 mMHEPES1reservoirpH7.
9PEG80001reservoir
10200 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→49.7 Å / Num. all: 14816 / Num. obs: 14742 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.5
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 152538 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.33

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→15 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 1384 random
Rwork0.219 --
all-14337 -
obs-13936 -
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 27 45 3420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.397 211 -
Rwork0.345 --
obs-1969 94.2 %
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Rfactor Rfree: 0.397 / Rfactor Rwork: 0.345

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