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- PDB-5v4l: Cryptococcus neoformans adenylosuccinate lyase -

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Basic information

Entry
Database: PDB / ID: 5v4l
TitleCryptococcus neoformans adenylosuccinate lyase
ComponentsAdenylosuccinate lyase
KeywordsLYASE / fumerase / adenylosuccinate / SAICAR
Function / homology
Function and homology information


adenylosuccinate lyase / N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity / (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido) succinate lyase (fumarate-forming) activity / 'de novo' AMP biosynthetic process / 'de novo' IMP biosynthetic process
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1570 / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1570 / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase C-terminal / Adenylosuccinate lyase C-terminus / Adenylosuccinate lyase / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Adenylosuccinate lyase
Similarity search - Component
Biological speciesCryptococcus neoformans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChitty, J. / Williams, S.J. / Kobe, B. / Fraser, J.A.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1049716 Australia
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Cryptococcus neoformans ADS lyase is an enzyme essential for virulence whose crystal structure reveals features exploitable in antifungal drug design.
Authors: Chitty, J.L. / Blake, K.L. / Blundell, R.D. / Koh, Y.Q.A.E. / Thompson, M. / Robertson, A.A.B. / Butler, M.S. / Cooper, M.A. / Kappler, U. / Williams, S.J. / Kobe, B. / Fraser, J.A.
History
DepositionMar 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 lyase
B: Adenylosuccinate lyase
C: Adenylosuccinate lyase
D: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)214,8494
Polymers214,8494
Non-polymers00
Water28,4281578
1
A: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)53,7121
Polymers53,7121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)53,7121
Polymers53,7121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)53,7121
Polymers53,7121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)53,7121
Polymers53,7121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29170 Å2
ΔGint-126 kcal/mol
Surface area62940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.110, 93.500, 159.250
Angle α, β, γ (deg.)90.00, 97.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Adenylosuccinate lyase / ASL / Adenylosuccinase


Mass: 53712.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (fungus)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: J9VSX1, adenylosuccinate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1578 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris/citric acid pH 6.5, 17% PEG 3350 and 0.12 M sodium chloride

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→39.44 Å / Num. obs: 130683 / % possible obs: 98.6 % / Redundancy: 3.5 % / Net I/σ(I): 2.78

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FFX

4ffx


Resolution: 2.1→39.437 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 6476 4.96 %
Rwork0.1567 --
obs0.1594 130631 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14412 0 0 1578 15990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714699
X-RAY DIFFRACTIONf_angle_d1.02219897
X-RAY DIFFRACTIONf_dihedral_angle_d13.6985459
X-RAY DIFFRACTIONf_chiral_restr0.0392254
X-RAY DIFFRACTIONf_plane_restr0.0052566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.28692300.22463942X-RAY DIFFRACTION95
2.1239-2.14880.25661830.22013983X-RAY DIFFRACTION95
2.1488-2.17510.28932300.21193982X-RAY DIFFRACTION95
2.1751-2.20260.25441890.2093905X-RAY DIFFRACTION96
2.2026-2.23160.3032250.20334043X-RAY DIFFRACTION95
2.2316-2.26210.261980.20454000X-RAY DIFFRACTION97
2.2621-2.29440.27162250.19194082X-RAY DIFFRACTION96
2.2944-2.32870.26032150.18794034X-RAY DIFFRACTION97
2.3287-2.36510.25282180.18974081X-RAY DIFFRACTION97
2.3651-2.40380.26591910.18054114X-RAY DIFFRACTION98
2.4038-2.44530.2522380.17674119X-RAY DIFFRACTION99
2.4453-2.48970.26432090.17754152X-RAY DIFFRACTION99
2.4897-2.53760.21782400.17024167X-RAY DIFFRACTION99
2.5376-2.58940.25952100.1664186X-RAY DIFFRACTION100
2.5894-2.64570.20362230.16284097X-RAY DIFFRACTION100
2.6457-2.70720.24082080.16354245X-RAY DIFFRACTION100
2.7072-2.77490.23642080.16054180X-RAY DIFFRACTION100
2.7749-2.84990.21512090.15884198X-RAY DIFFRACTION100
2.8499-2.93380.24422260.1614194X-RAY DIFFRACTION100
2.9338-3.02840.23582280.164182X-RAY DIFFRACTION100
3.0284-3.13660.21332120.15584195X-RAY DIFFRACTION100
3.1366-3.26210.20212210.15444210X-RAY DIFFRACTION100
3.2621-3.41050.20982010.15134213X-RAY DIFFRACTION100
3.4105-3.59020.19232200.14394211X-RAY DIFFRACTION100
3.5902-3.8150.18212160.13694188X-RAY DIFFRACTION100
3.815-4.10930.16052390.1244222X-RAY DIFFRACTION100
4.1093-4.52230.15192180.11624210X-RAY DIFFRACTION100
4.5223-5.17540.16832050.11634263X-RAY DIFFRACTION100
5.1754-6.51570.17682080.14984264X-RAY DIFFRACTION100
6.5157-39.44380.15782330.13924293X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 11.515 Å / Origin y: 10.7526 Å / Origin z: 43.0767 Å
111213212223313233
T-0.0102 Å2-0.042 Å2-0.0188 Å2--0.0332 Å2-0.0336 Å2---0.015 Å2
L0.0719 °20.0291 °20.0046 °2-0.0952 °2-0.0206 °2--0.0674 °2
S-0.0027 Å °0.0099 Å °-0.0168 Å °-0.0866 Å °-0.0466 Å °0.0049 Å °0.0744 Å °0.0124 Å °-0.086 Å °
Refinement TLS groupSelection details: all

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