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- PDB-6u4o: Crystal structure of recombinant class II fumarase from Schistoso... -

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Basic information

Entry
Database: PDB / ID: 6u4o
TitleCrystal structure of recombinant class II fumarase from Schistosoma mansoni
ComponentsFumarate hydratase
KeywordsLYASE / SmFHII / fumarate hydratase
Function / homology
Function and homology information


tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
ACETATE ION / (2S)-2-hydroxybutanedioic acid / Fumarate hydratase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCardoso, I.A. / Nonato, M.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)308058/2012-7 Brazil
Sao Paulo Research Foundation (FAPESP)2008/08262-6 Brazil
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Characterization of class II fumarase from Schistosoma mansoni provides the molecular basis for selective inhibition.
Authors: Cardoso, I.A. / de Souza, A.K.L. / Burgess, A.M.G. / Chalmers, I.W. / Hoffmann, K.F. / Nonato, M.C.
History
DepositionAug 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: 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.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
C: Fumarate hydratase
A: Fumarate hydratase
D: Fumarate hydratase
B: Fumarate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,48116
Polymers215,3404
Non-polymers1,14112
Water16,087893
1
C: Fumarate hydratase
D: Fumarate hydratase
hetero molecules

C: Fumarate hydratase
D: Fumarate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,29614
Polymers215,3404
Non-polymers95710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area32380 Å2
ΔGint-214 kcal/mol
Surface area56440 Å2
MethodPISA
2
A: Fumarate hydratase
B: Fumarate hydratase
hetero molecules

A: Fumarate hydratase
B: Fumarate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,66518
Polymers215,3404
Non-polymers1,32514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area34870 Å2
ΔGint-220 kcal/mol
Surface area56570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.650, 67.860, 187.270
Angle α, β, γ (deg.)90.000, 118.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Fumarate hydratase


Mass: 53834.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_158240 / Plasmid: pET28a-SUMO / Details (production host): pET28a-SUMO modified vector / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5K4ESW0*PLUS, fumarate hydratase
#2: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 893 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: Sodium acetate pH 4, sodium L-malate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.85→46.93 Å / Num. obs: 167349 / % possible obs: 98.6 % / Redundancy: 6.8 % / CC1/2: 0.997 / Net I/σ(I): 11.2
Reflection shellResolution: 1.85→1.9 Å / Num. unique obs: 11054 / CC1/2: 0.552

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d6b

5d6b


Resolution: 1.85→46.93 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.223 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.134
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 8368 5 %RANDOM
Rwork0.1918 ---
obs0.1936 158981 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 99.18 Å2 / Biso mean: 29.562 Å2 / Biso min: 11.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å20.58 Å2
2---1.51 Å20 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 1.85→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14331 0 124 900 15355
Biso mean--34.99 34.05 -
Num. residues----1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01314713
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713539
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.63219975
X-RAY DIFFRACTIONr_angle_other_deg1.2981.56731446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92451926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44523.522636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.299152483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4711562
X-RAY DIFFRACTIONr_chiral_restr0.0680.22016
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022780
LS refinement shellResolution: 1.851→1.899 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 551 -
Rwork0.396 10468 -
all-11019 -
obs--88.24 %

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