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- PDB-5eyv: Crystal Structure of Adenylosuccinate lyase from Schistosoma mans... -

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Basic information

Entry
Database: PDB / ID: 5eyv
TitleCrystal Structure of Adenylosuccinate lyase from Schistosoma mansoni in APO form.
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
Adenylosuccinate lyase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 Å
AuthorsRomanello, L. / Torini, J.R. / Bird, L.E. / Nettleship, J.E. / Owens, R.J. / 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

Downloads & links

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Assembly

Deposited unit
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)113,1372
Polymers113,1372
Non-polymers00
Water7,152397
1
A: Adenylosuccinate lyase
B: Adenylosuccinate lyase

A: Adenylosuccinate lyase
B: Adenylosuccinate lyase


Theoretical massNumber of molelcules
Total (without water)226,2744
Polymers226,2744
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area26260 Å2
ΔGint-93 kcal/mol
Surface area61280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.160, 82.630, 163.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-593-

HOH

21B-615-

HOH

31B-634-

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.: 2
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): Lemo21 / References: UniProt: G4VQX9, adenylosuccinate lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM Mes/imidazole pH 6.5, 10%, 20% Ethylene glycol, 20mM of each D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.14→82.63 Å / Num. obs: 57766 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible all
2.14-2.27.10.7431099.9
9.57-82.636.70.0491098.7

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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: 5EYT

5eyt


Resolution: 2.14→58.165 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 2903 5.03 %Random selection
Rwork0.2224 54827 --
obs0.2241 57730 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.72 Å2 / Biso mean: 51.07 Å2 / Biso min: 7.95 Å2
Refinement stepCycle: final / Resolution: 2.14→58.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6871 0 0 397 7268
Biso mean---47.63 -
Num. residues----886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026993
X-RAY DIFFRACTIONf_angle_d0.4939481
X-RAY DIFFRACTIONf_chiral_restr0.0371117
X-RAY DIFFRACTIONf_plane_restr0.0031208
X-RAY DIFFRACTIONf_dihedral_angle_d12.7064264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.17510.3091480.285225842732100
2.1751-2.21260.29031360.275225522688100
2.2126-2.25280.28651540.260125792733100
2.2528-2.29620.35471190.260225992718100
2.2962-2.34310.32661350.252525592694100
2.3431-2.3940.30631370.254425862723100
2.394-2.44970.26141240.24426112735100
2.4497-2.5110.24761460.242425802726100
2.511-2.57880.24561270.23725922719100
2.5788-2.65470.24911480.232225692717100
2.6547-2.74040.32121390.244626112750100
2.7404-2.83840.29981120.239526252737100
2.8384-2.9520.28411280.243426252753100
2.952-3.08630.28741460.238525592705100
3.0863-3.2490.23591330.23382575270899
3.249-3.45260.25551590.222426142773100
3.4526-3.71910.22671360.207426162752100
3.7191-4.09330.20981250.198126612786100
4.0933-4.68540.22981830.185626262809100
4.6854-5.90220.23161600.20592665282599
5.9022-58.18630.25971080.2022839294799
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)
10.46630.6774-0.59051.2105-0.63521.18910.02190.91951.0018-0.5526-0.6022-0.0283-0.5289-0.0811-0.67880.71470.01610.19590.7361.06821.1337-28.856430.855-54.3698
22.1296-0.03760.10860.6783-0.25831.83930.06310.540.4131-0.1084-0.0233-0.0702-0.29550.1751-0.07030.2668-0.01590.03380.25530.09130.2969-25.183312.0098-37.4645
30.6665-0.3783-0.07481.9058-0.77440.956-0.1756-0.5011-0.26030.40890.1139-0.078-0.00580.05660.0160.32920.0326-0.02270.41740.13080.3623-24.3078-11.65624.4999
42.19360.223-0.98280.61490.35892.1340.0191-0.08990.67420.14830.15760.119-0.4236-0.0438-0.00140.2572-0.0144-0.02230.25240.03570.4678-14.66489.7541-17.7086
52.1242-0.44840.70970.84080.28651.8240.2356-0.1674-1.34030.1029-0.08670.06340.654-0.1836-0.11380.50450.0055-0.01520.29110.0520.9019-17.9987-25.8243-26.7427
62.2296-0.1915-0.46180.3473-0.2341.16360.10670.952-0.2155-0.1304-0.1214-0.1196-0.0015-0.10620.11590.29040.05030.03870.5241-0.08240.2189-22.5287-4.8918-48.0638
71.3156-0.37560.31181.4965-0.55671.9480.17080.83960.0233-0.32750.16650.2346-0.06620.2232-0.21370.44880.01960.08181.2916-0.01110.461-14.84632.4896-68.0683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 105 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 356 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 357 through 439 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 440 through 479 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 105 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 386 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 387 through 479 )B0

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