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- PDB-5eyt: Crystal Structure of Adenylosuccinate Lyase from Schistosoma mans... -

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Basic information

Entry
Database: PDB / ID: 5eyt
TitleCrystal Structure of Adenylosuccinate Lyase from Schistosoma mansoni in complex with AMP
ComponentsAdenylosuccinate lyase
KeywordsLYASE
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 / nucleotide binding
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
ADENOSINE MONOPHOSPHATE / Adenylosuccinate lyase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3649 Å
AuthorsRomanello, L. / Torini, J.R. / Bird, L. / Nettleship, J. / Owens, R. / Reddivari, Y. / Brandao-Neto, J. / Pereira, H.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)474402/2013-4 Brazil
CitationJournal: Mol. Biochem. Parasitol. / Year: 2017
Title: Structural and kinetic analysis of Schistosoma mansoni Adenylosuccinate Lyase (SmADSL).
Authors: Romanello, L. / Serrao, V.H. / Torini, J.R. / Bird, L.E. / Nettleship, J.E. / Rada, H. / Reddivari, Y. / Owens, R.J. / DeMarco, R. / Brandao-Neto, J. / Pereira, H.D.
History
DepositionNov 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Data collection
Category: diffrn_source / pdbx_struct_assembly_auth_evidence
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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

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Assembly

Deposited unit
A: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9162
Polymers56,5681
Non-polymers3471
Water2,360131
1
A: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
hetero molecules

A: Adenylosuccinate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,6638
Polymers226,2744
Non-polymers1,3894
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area34600 Å2
ΔGint-150 kcal/mol
Surface area61120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.466, 73.114, 180.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1207-

HOH

DetailsTetramer confirmed by Gel filtration/DLS

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Components

#1: Protein Adenylosuccinate lyase / ASL / Adenylosuccinase


Mass: 56568.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_038030 / Plasmid: pOPINF / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo 21 / References: UniProt: G4VQX9, adenylosuccinate lyase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Tris base/bicine, 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350, 30mM of each diethylene glycol, triethylene glycol, tetraethylene glycol and pentaethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.36→35.23 Å / Num. obs: 19416 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 8.5 / Scaling rejects: 116
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible all
2.36-2.495.60.6511099.9
7.48-35.235.10.0451098.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J91

2j91


Resolution: 2.3649→35.23 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 992 5.11 %Random selection
Rwork0.1916 18407 --
obs0.1937 19399 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.14 Å2 / Biso mean: 40.9594 Å2 / Biso min: 15.81 Å2
Refinement stepCycle: final / Resolution: 2.3649→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 23 131 3889
Biso mean--41.42 41.55 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023829
X-RAY DIFFRACTIONf_angle_d0.5445182
X-RAY DIFFRACTIONf_chiral_restr0.038597
X-RAY DIFFRACTIONf_plane_restr0.003656
X-RAY DIFFRACTIONf_dihedral_angle_d12.9842343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3649-2.48950.29661570.24892558X-RAY DIFFRACTION100
2.4895-2.64550.30461350.24572597X-RAY DIFFRACTION100
2.6455-2.84960.28521480.23652583X-RAY DIFFRACTION100
2.8496-3.13620.28861390.22332612X-RAY DIFFRACTION99
3.1362-3.58970.25231240.20032637X-RAY DIFFRACTION99
3.5897-4.52110.20091380.15282659X-RAY DIFFRACTION100
4.5211-35.230.17081510.16252761X-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)
11.51330.5169-0.15411.340.30881.94830.2873-0.26850.50270.3815-0.15550.2184-0.4034-0.0582-0.05970.4582-0.04720.09510.2817-0.05730.4777-14.072-7.833414.1526
20.7047-0.0954-0.16150.45480.26751.67660.054-0.01940.04630.0091-0.08170.1464-0.0291-0.1816-0.00960.2098-0.00340.01620.2373-0.00140.3076-18.8798-27.9592-1.6548
31.2577-0.2086-0.47360.23360.14543.63850.14180.17090.1175-0.0753-0.1099-0.0259-0.09170.1458-0.08440.21440.0072-0.00060.1573-0.00320.2448-4.4133-26.4699-9.6853
40.46160.03730.07590.53510.14161.09350.08370.2012-0.0424-0.1737-0.05970.05320.0864-0.21420.01430.28090.02570.00630.33870.02570.2849-11.233-35.921-25.2069
50.8567-0.1666-0.31811.35610.92861.38270.06090.3149-0.2074-0.273-0.06280.09120.0544-0.1694-0.01360.36350.0352-0.11350.4706-0.02470.3655-14.0094-44.4436-35.8379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 105 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 269 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 270 through 328 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 329 through 391 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 392 through 480 )A0

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