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- PDB-1loo: Crystal Structure of the Mouse-Muscle Adenylosuccinate Synthetase... -

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Basic information

Entry
Database: PDB / ID: 1loo
TitleCrystal Structure of the Mouse-Muscle Adenylosuccinate Synthetase Ligated with GTP
Componentsadenylosuccinate synthetase
KeywordsLIGASE / Purine biosynthesis / GTP-binding
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
GUANOSINE-5'-TRIPHOSPHATE / Adenylosuccinate synthetase isozyme 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsIancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: IMP, GTP, and 6-phosphoryl-IMP complexes of recombinant mouse muscle adenylosuccinate synthetase.
Authors: Iancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B.
History
DepositionMay 6, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 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 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)50,8442
Polymers50,3211
Non-polymers5231
Water1,802100
1
A: adenylosuccinate synthetase
hetero molecules

A: adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6894
Polymers100,6432
Non-polymers1,0462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area7550 Å2
ΔGint-32 kcal/mol
Surface area32040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.935, 69.935, 198.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a dimer. The asymmetric unit contains one monomer. The other monomer is generated by the symmetry operation: -y, -x, 1/2-z.

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Components

#1: Protein adenylosuccinate synthetase


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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, magnesium acetate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlenzyme1drop
250 mMHEPES1droppH7.5
350 mM1dropNaCl
41 mMdithiothreitol1drop
50.5 mMEDTA1drop
65 mMGTP1drop
7200 mMmagnesium acetate1reservoir
8100 mMHEPES1reservoirpH7.0
918 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 19, 2002 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→65.9 Å / Num. all: 25715 / Num. obs: 21799 / % possible obs: 91.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 47.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2124 / % possible all: 89.5
Reflection
*PLUS
Num. obs: 25715 / % possible obs: 89.5 % / Num. measured all: 126081 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Lowest resolution: 2.3 Å / % possible obs: 98.5 % / Rmerge(I) obs: 0.312

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J4B

1j4b


Resolution: 2.2→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.276 2505 random
Rwork0.244 --
all-25407 -
obs-23247 -
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.25 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 32 100 3485
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection
Rfree0.382 376
Rwork0.338 -
obs-3684
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 25407 / % reflection Rfree: 10 % / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rfree: 0.382 / Rfactor Rwork: 0.338

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