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- PDB-1mf0: Structure of the Recombinant Mouse-Muscle Adenylosuccinate Synthe... -

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Basic information

Entry
Database: PDB / ID: 1mf0
TitleStructure of the Recombinant Mouse-Muscle Adenylosuccinate Synthetase Complexed with AMP, GDP, HPO4(2-), and Mg(2+)
ComponentsAdenylosuccinate SynthetaseAdenylosuccinate synthase
KeywordsLIGASE / Purine biosynthesis / GTP-binding / Multigene family
Function / homology
Function and homology information


Purine ribonucleoside monophosphate biosynthesis / AMP biosynthetic process / adenylosuccinate synthase / adenylosuccinate synthase activity / purine nucleotide metabolic process / aspartate metabolic process / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / actin filament binding ...Purine ribonucleoside monophosphate biosynthesis / AMP biosynthetic process / adenylosuccinate synthase / adenylosuccinate synthase activity / purine nucleotide metabolic process / aspartate metabolic process / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / actin filament binding / GTPase activity / GTP binding / magnesium ion binding / membrane / identical protein binding / cytoplasm
Similarity search - Function
Adenylosuccinate synthetase isozyme 1, chordates / 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 isozyme 1, chordates / 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
ADENOSINE MONOPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Adenylosuccinate synthetase isozyme 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)51,2315
Polymers50,3211
Non-polymers9104
Water1,928107
1
A: Adenylosuccinate Synthetase
hetero molecules

A: Adenylosuccinate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,46210
Polymers100,6432
Non-polymers1,8198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area9230 Å2
ΔGint-84 kcal/mol
Surface area29290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.600, 70.600, 198.390
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

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Protein , 1 types, 1 molecules A

#1: Protein Adenylosuccinate Synthetase / Adenylosuccinate synthase / 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

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Non-polymers , 5 types, 111 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
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
65 mMAMP1drop
75 mMGDP1drop
825 mMpotassium phosphate1drop
910 mMmagnesium acetate1drop
10100 mMHEPES1reservoirpH7.
12200 mMmagnesium acetate1reservoir
11PEG80001reservoir

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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: 2.5→48 Å / Num. all: 18234 / Num. obs: 18179 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7
Reflection shellResolution: 2.5→2.6 Å / % possible all: 100
Reflection
*PLUS
Lowest resolution: 48.3 Å / Num. measured all: 101321 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.341

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→15 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.292 1738 random
Rwork0.219 --
all-18105 -
obs-17562 -
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 57 107 3517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.358 273 -
Rwork0.297 --
obs-2507 95.2 %
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 17563 / % reflection Rfree: 10 % / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.216
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_deg0.83
LS refinement shell
*PLUS
Highest resolution: 2.5 Å

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