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- PDB-5i34: Adenylosuccinate synthetase from Cryptococcus neoformans complexe... -

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Basic information

Entry
Database: PDB / ID: 5i34
TitleAdenylosuccinate synthetase from Cryptococcus neoformans complexed with GDP and IMP
ComponentsAdenylosuccinate synthetaseAdenylosuccinate synthase
KeywordsLIGASE / dimer / adenylosuccinate synthetase / purine metabolism
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, 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
GUANOSINE-5'-DIPHOSPHATE / INOSINIC ACID / Adenylosuccinate synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsBlundell, R.D. / Williams, S.J. / Ericsson, D. / Fraser, J.A. / Kobe, B.
CitationJournal: Acs Infect Dis. / Year: 2016
Title: Disruption of de Novo Adenosine Triphosphate (ATP) Biosynthesis Abolishes Virulence in Cryptococcus neoformans.
Authors: Blundell, R.D. / Williams, S.J. / Arras, S.D. / Chitty, J.L. / Blake, K.L. / Ericsson, D.J. / Tibrewal, N. / Rohr, J. / Koh, Y.Q. / Kappler, U. / Robertson, A.A. / Butler, M.S. / Cooper, M.A. ...Authors: Blundell, R.D. / Williams, S.J. / Arras, S.D. / Chitty, J.L. / Blake, K.L. / Ericsson, D.J. / Tibrewal, N. / Rohr, J. / Koh, Y.Q. / Kappler, U. / Robertson, A.A. / Butler, M.S. / Cooper, M.A. / Kobe, B. / Fraser, J.A.
History
DepositionFeb 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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)97,4626
Polymers95,8792
Non-polymers1,5834
Water14,502805
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-41 kcal/mol
Surface area29640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.807, 100.774, 163.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adenylosuccinate synthetase / Adenylosuccinate synthase


Mass: 47939.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_02858 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: J9VI09, adenylosuccinate synthase
#2: 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
#3: Chemical ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 2.47 Å3/Da / Density % sol: 50.15 % / Description: Long, rectangular "chisel-shaped" crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M ammonium citrate tribasic 18% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.53→46.12 Å / Num. obs: 140564 / % possible obs: 99.93 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.6
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.68 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I33

5i33


Resolution: 1.53→46.118 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 16.79
RfactorNum. reflection% reflection
Rfree0.1856 2000 1.42 %
Rwork0.1339 --
obs0.1347 140560 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.53→46.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6430 0 102 805 7337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096673
X-RAY DIFFRACTIONf_angle_d1.1849052
X-RAY DIFFRACTIONf_dihedral_angle_d12.392408
X-RAY DIFFRACTIONf_chiral_restr0.0471010
X-RAY DIFFRACTIONf_plane_restr0.0061153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.56520.25531400.1869694X-RAY DIFFRACTION99
1.5652-1.60750.23711410.16529769X-RAY DIFFRACTION100
1.6075-1.65480.24771420.15839839X-RAY DIFFRACTION100
1.6548-1.70830.22271410.14499805X-RAY DIFFRACTION100
1.7083-1.76930.20451420.13489804X-RAY DIFFRACTION100
1.7693-1.84020.1631420.12749820X-RAY DIFFRACTION100
1.8402-1.92390.15751420.12459893X-RAY DIFFRACTION100
1.9239-2.02530.20531420.12999818X-RAY DIFFRACTION100
2.0253-2.15220.18351420.12729885X-RAY DIFFRACTION100
2.1522-2.31840.18741430.12259890X-RAY DIFFRACTION100
2.3184-2.55170.15951440.12389929X-RAY DIFFRACTION100
2.5517-2.92090.18011440.13689966X-RAY DIFFRACTION100
2.9209-3.67980.19831450.13710054X-RAY DIFFRACTION100
3.6798-46.1390.16411500.130810394X-RAY DIFFRACTION100

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