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- PDB-6w53: Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC070) -

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Basic information

Entry
Database: PDB / ID: 6w53
TitleTrypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC070)
ComponentsMalic enzyme
KeywordsOXIDOREDUCTASE/Inhibitor / Inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


malate dehydrogenase (decarboxylating) (NAD+) activity / malate metabolic process / pyruvate metabolic process / NAD binding / mitochondrion / metal ion binding
Similarity search - Function
Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain ...Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-SZP / Malic enzyme
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMercaldi, G.F. / Fagundes, M. / Faria, J.N. / Cordeiro, A.T.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)16/14271-4 Brazil
Sao Paulo Research Foundation (FAPESP)18/22202-8 Brazil
Sao Paulo Research Foundation (FAPESP)16/03151-8 Brazil
CitationJournal: Acs Infect Dis. / Year: 2021
Title: Trypanosoma cruzi Malic Enzyme Is the Target for Sulfonamide Hits from the GSK Chagas Box.
Authors: Mercaldi, G.F. / Eufrasio, A.G. / Ranzani, A.T. / do Nascimento Faria, J. / Mota, S.G.R. / Fagundes, M. / Bruder, M. / Cordeiro, A.T.
History
DepositionMar 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3563
Polymers61,6101
Non-polymers7452
Water4,071226
1
A: Malic enzyme
hetero molecules

A: Malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7116
Polymers123,2212
Non-polymers1,4904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area5330 Å2
ΔGint-11 kcal/mol
Surface area42000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.172, 73.172, 233.069
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

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Components

#1: Protein Malic enzyme


Mass: 61610.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_11g406 / Plasmid: pET_SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V2XFZ1
#2: Chemical ChemComp-SZP / N-(2-chloro-5-{[4-(trifluoromethoxy)phenyl]sulfamoyl}phenyl)-3,5-difluorobenzamide


Mass: 506.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12ClF5N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.53 Å3/Da / Density % sol: 51.42 % / Mosaicity: 0.27 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES, 1.2-1.4 M Na3-Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4587 Å / Relative weight: 1
ReflectionResolution: 2.1→47.29 Å / Num. obs: 35984 / % possible obs: 95.1 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.033 / Rrim(I) all: 0.082 / Net I/σ(I): 14.4 / Num. measured all: 218672 / Scaling rejects: 36
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.515 / Num. measured all: 10575 / Num. unique obs: 2272 / CC1/2: 0.804 / Rpim(I) all: 0.249 / Rrim(I) all: 0.576 / Net I/σ(I) obs: 2.4 / % possible all: 75

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
MxCuBEdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6W29

6w29


Resolution: 2.1→36.17 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.425 / SU ML: 0.115 / SU R Cruickshank DPI: 0.2074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.162
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 1697 4.7 %RANDOM
Rwork0.1813 ---
obs0.1825 34260 94.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.22 Å2 / Biso mean: 36.451 Å2 / Biso min: 23.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å2-0 Å2-0 Å2
2--0.58 Å2-0 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 2.1→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4226 0 48 226 4500
Biso mean--37.52 40.06 -
Num. residues----540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134360
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174109
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.6645914
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5819519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90822.172221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42115742
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3751529
X-RAY DIFFRACTIONr_chiral_restr0.080.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024842
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02908
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 101 -
Rwork0.262 1923 -
all-2024 -
obs--73.02 %

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