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- PDB-6jrq: Crystal structure of adenylosuccinate synthetase, PurA, from Ther... -

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Basic information

Entry
Database: PDB / ID: 6jrq
TitleCrystal structure of adenylosuccinate synthetase, PurA, from Thermus thermophilus
ComponentsAdenylosuccinate synthetase
KeywordsLIGASE / purine / IMP / complex / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
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, GTP-binding site / Adenylosuccinate synthetase, domain 2 / Adenylosuccinate synthetase, domain 3 / Adenylosuccinate synthetase GTP-binding site. / Adenylosuccinate synthetase / Adenylosuccinate synthetase, 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, 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 / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSampei, G. / Kawai, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To Be Published
Title: Crystal structure of adenylosuccinate synthetase, PurA, from Thermus thermophilus HB8
Authors: Ishii, H. / Taka, H. / Kawai, G. / Sampei, G.
History
DepositionApr 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
B: Adenylosuccinate synthetase
C: Adenylosuccinate synthetase
D: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,80218
Polymers179,7884
Non-polymers2,01414
Water10,251569
1
A: Adenylosuccinate synthetase
B: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,96310
Polymers89,8942
Non-polymers1,0698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint9 kcal/mol
Surface area28920 Å2
MethodPISA
2
C: Adenylosuccinate synthetase
D: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,8398
Polymers89,8942
Non-polymers9456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint3 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.850, 106.390, 114.530
Angle α, β, γ (deg.)90.00, 96.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Adenylosuccinate synthetase / AdSS / IMP--aspartate ligase


Mass: 44947.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q5SLS1, adenylosuccinate synthase
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: PEG 8000, Ethylene Glycol, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→34.47 Å / Num. obs: 101788 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 8.754 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.048 / Rrim(I) all: 0.082 / Net I/σ(I): 14
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5002 / CC1/2: 0.97 / Rpim(I) all: 0.119 / Rrim(I) all: 0.206 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
MOSFLMdata reduction
Aimless0.2.8data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DJ3

1dj3


Resolution: 2.1→34.47 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.893 / SU B: 4.9 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22636 5094 5 %RANDOM
Rwork0.18332 ---
obs0.18549 96693 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.368 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12660 0 132 569 13361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01913079
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212414
X-RAY DIFFRACTIONr_angle_refined_deg1.8641.97617725
X-RAY DIFFRACTIONr_angle_other_deg1.075328585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51351626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7822.239585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.946152143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.19315137
X-RAY DIFFRACTIONr_chiral_restr0.1990.21949
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114580
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022797
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6941.8746510
X-RAY DIFFRACTIONr_mcbond_other1.6941.8746509
X-RAY DIFFRACTIONr_mcangle_it2.7092.8048131
X-RAY DIFFRACTIONr_mcangle_other2.7092.8048132
X-RAY DIFFRACTIONr_scbond_it2.1732.196569
X-RAY DIFFRACTIONr_scbond_other2.1732.196570
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4973.1639594
X-RAY DIFFRACTIONr_long_range_B_refined5.05522.02714470
X-RAY DIFFRACTIONr_long_range_B_other5.05522.02814471
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 390 -
Rwork0.193 7065 -
obs--98.38 %

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