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- PDB-3hid: Crystal structure of adenylosuccinate synthetase from Yersinia pe... -

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Basic information

Entry
Database: PDB / ID: 3hid
TitleCrystal structure of adenylosuccinate synthetase from Yersinia pestis CO92
ComponentsAdenylosuccinate synthetaseAdenylosuccinate synthase
KeywordsLIGASE / NIAID Structural Genomics / adenylosuccinate synthetase / Virulence Associated Factor / purA / purine ribonucleotide biosynthesis / Cytoplasm / GTP-binding / Magnesium / Metal-binding / Nucleotide-binding / Purine biosynthesis / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


adenylosuccinate synthase / adenylosuccinate synthase activity / IMP metabolic process / 'de novo' AMP biosynthetic process / GTP binding / magnesium ion binding / cytoplasm
Similarity search - Function
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, 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
Chem-PG6 / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Zhou, M. / Peterson, S. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of the adenylosuccinate synthetase from Yersinia pestis CO92
Authors: Zhang, R. / Zhou, M. / Peterson, S. / Anderson, W. / Joachimiak, A.
History
DepositionMay 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6002
Polymers47,3341
Non-polymers2661
Water11,728651
1
A: Adenylosuccinate synthetase
hetero molecules

A: Adenylosuccinate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2004
Polymers94,6682
Non-polymers5332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area5270 Å2
ΔGint-20.1 kcal/mol
Surface area31320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.903, 68.903, 199.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 47333.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Biovar Orientalis / Gene: gi:16120713, purA, y0635, YPO0378, YP_0534 / Plasmid: pMCSG19c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8ZIV7, adenylosuccinate synthase
#2: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE / Polyethylene glycol


Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 651 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 30% w/v PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2008 / Details: mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→56.7 Å / Num. all: 60980 / Num. obs: 60809 / % possible obs: 99.72 % / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 35.46
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4655 / % possible all: 98.24

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→56.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.82 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.105 / ESU R Free: 0.083
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19756 3235 5.1 %RANDOM
Rwork0.16022 ---
obs0.16213 60809 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.996 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→56.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 9 651 3938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223348
X-RAY DIFFRACTIONr_bond_other_d0.0010.022266
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9794536
X-RAY DIFFRACTIONr_angle_other_deg0.97535526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8823.878147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04115574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4361526
X-RAY DIFFRACTIONr_chiral_restr0.0980.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213725
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02657
X-RAY DIFFRACTIONr_mcbond_it1.4241.52093
X-RAY DIFFRACTIONr_mcbond_other0.6141.5873
X-RAY DIFFRACTIONr_mcangle_it2.22723372
X-RAY DIFFRACTIONr_scbond_it3.39731255
X-RAY DIFFRACTIONr_scangle_it4.7454.51164
X-RAY DIFFRACTIONr_rigid_bond_restr1.73835614
X-RAY DIFFRACTIONr_sphericity_free6.83704
X-RAY DIFFRACTIONr_sphericity_bonded3.41535558
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 214 -
Rwork0.201 4359 -
obs-4573 98.24 %

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