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- PDB-5i33: Unligated adenylosuccinate synthetase from Cryptococcus neoformans -

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Basic information

Entry
Database: PDB / ID: 5i33
TitleUnligated adenylosuccinate synthetase from Cryptococcus neoformans
ComponentsAdenylosuccinate synthetase
KeywordsLIGASE / dimer / adenylosuccinate synthetase / purine metabolism
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 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Adenylosuccinate synthetase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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


Theoretical massNumber of molelcules
Total (without water)95,8792
Polymers95,8792
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-20 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.083, 101.040, 163.845
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


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 / Plasmid: PQE30 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: J9VI09, adenylosuccinate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Description: Long rectangular crystals, approximately 0.5 by 0.05 by 0.05 mm
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M bis-tris propane pH 8 0.2 M sodium bromide 17% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.2→37.02 Å / Num. obs: 49839 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.8
Reflection shellHighest resolution: 2.2 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J4B

1j4b


Resolution: 2.2→37.02 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.39
RfactorNum. reflection% reflection
Rfree0.243 1993 4.01 %
Rwork0.2064 --
obs0.2079 49693 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→37.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5823 0 0 85 5908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095940
X-RAY DIFFRACTIONf_angle_d1.1168039
X-RAY DIFFRACTIONf_dihedral_angle_d12.4312143
X-RAY DIFFRACTIONf_chiral_restr0.046912
X-RAY DIFFRACTIONf_plane_restr0.0061028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.32831400.30773354X-RAY DIFFRACTION100
2.255-2.3160.32641400.28063362X-RAY DIFFRACTION100
2.316-2.38410.33171380.26013322X-RAY DIFFRACTION100
2.3841-2.46110.30631400.24913346X-RAY DIFFRACTION99
2.4611-2.5490.27211420.2333391X-RAY DIFFRACTION100
2.549-2.6510.30541420.23283389X-RAY DIFFRACTION100
2.651-2.77160.29631410.2363362X-RAY DIFFRACTION100
2.7716-2.91770.31441420.25413392X-RAY DIFFRACTION100
2.9177-3.10040.3311410.24183381X-RAY DIFFRACTION100
3.1004-3.33970.30881420.24433410X-RAY DIFFRACTION100
3.3397-3.67550.26581420.21143421X-RAY DIFFRACTION100
3.6755-4.20670.18541450.17543459X-RAY DIFFRACTION100
4.2067-5.29750.20431470.15823502X-RAY DIFFRACTION100
5.2975-37.02640.18321510.18633609X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.00141.0156-0.90032.26980.66082.7818-0.06030.146-0.3777-0.1360.05910.06440.8153-0.33510.0010.6072-0.0707-0.06380.4864-0.01650.459239.609436.2144114.1463
22.03730.2148-0.43452.205-0.84153.4630.0204-0.1956-0.504-0.1701-0.0895-0.17641.0619-0.14230.09180.72970.0383-0.04860.42-0.01550.520649.544630.4575103.4214
31.29480.0127-0.58291.1422-0.75125.44110.0076-0.1892-0.04580.06260.02680.04070.2631-0.0146-0.03570.4154-0.0374-0.03240.4276-0.01680.424741.432744.4345127.8888
40.33350.11860.30981.69280.5232.42740.3324-0.12620.2405-0.0563-0.0588-0.1241-0.57760.1866-0.2680.55650.0030.04270.473-0.03240.4546.244164.421396.7523
52.60960.07610.12562.5331-0.93332.32310.1409-0.13130.30890.2846-0.1809-0.4334-0.59760.52320.0520.5283-0.17870.00950.4642-0.05390.480657.178765.1215108.3395
61.4871-0.0391-0.5390.8882-1.17265.26250.07470.3330.0056-0.13520.05330.0856-0.0703-0.2048-0.11750.3719-0.0216-0.02580.39-0.02730.379844.712656.117382.9428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 233 )
3X-RAY DIFFRACTION3chain 'A' and (resid 234 through 430 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 47 )
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 233 )
6X-RAY DIFFRACTION6chain 'B' and (resid 234 through 430 )

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