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- PDB-1lny: Crystal structure of the recombinant mouse-muscle adenylosuccinat... -

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Basic information

Entry
Database: PDB / ID: 1lny
TitleCrystal structure of the recombinant mouse-muscle adenylosuccinate synthetase complexed with 6-phosphoryl-IMP, GDP and Mg
ComponentsAdenylosuccinate SynthetaseAdenylosuccinate synthase
KeywordsLIGASE / Purine biosynthesis / GTP-binding
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
GUANOSINE-5'-DIPHOSPHATE / 6-O-PHOSPHORYL INOSINE MONOPHOSPHATE / 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 4, 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: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate Synthetase
B: Adenylosuccinate Synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4348
Polymers100,6432
Non-polymers1,7916
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8850 Å2
ΔGint-64 kcal/mol
Surface area29520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.500, 70.120, 105.130
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer and it is contained by the asymmetric unit.

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Components

#1: Protein Adenylosuccinate Synthetase / Adenylosuccinate synthase


Mass: 50321.301 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IMO / 6-O-PHOSPHORYL INOSINE MONOPHOSPHATE


Mass: 428.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O11P2
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 400, magnesium acetate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
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 mMIMP1drop
7200 mMmagnesium acetate1reservoir
8100 mMHEPES1reservoirpH7.0
918-19 %(w/v)PEG33501reservoir

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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: Jul 20, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40.5 Å / Num. all: 50470 / Num. obs: 50176 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.29 Å / Redundancy: 3 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2 / % possible all: 79
Reflection
*PLUS
Num. obs: 48646 / % possible obs: 92.3 % / Num. measured all: 175127 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Lowest resolution: 2.3 Å / % possible obs: 86.5 % / Rmerge(I) obs: 0.222

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Processing

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

1j4b


Resolution: 2.2→5 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 4348 random
Rwork0.207 --
all-43159 -
obs-43159 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.44 Å2-3.8 Å2-8.6 Å2
2--0 Å2-3.99 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6701 0 112 317 7130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.2→2.32 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.321 720 -
Rwork0.289 --
obs-6190 95.7 %
Refinement
*PLUS
Lowest resolution: 5 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.207
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_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.321 / Rfactor Rwork: 0.289

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