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- PDB-6w2n: Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC009) -

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Basic information

Entry
Database: PDB / ID: 6w2n
TitleTrypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC009)
ComponentsMalic enzyme
KeywordsOXIDOREDUCTASE/Inhibitor / Inhibitor / isomerase / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex
Function / homology
Function and homology information


malate dehydrogenase (decarboxylating) (NAD+) activity / malate 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
CITRIC ACID / Chem-SJD / Malic enzyme
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 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)62,4774
Polymers61,6101
Non-polymers8673
Water6,071337
1
A: Malic enzyme
hetero molecules

A: Malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,9548
Polymers123,2212
Non-polymers1,7346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area6070 Å2
ΔGint-6 kcal/mol
Surface area43150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.835, 73.835, 234.506
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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 (strain CL Brener) (eukaryote)
Strain: CL Brener / Gene: Tc00.1047053505183.30 / Plasmid: pET_SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4DJ68
#2: Chemical ChemComp-SJD / 3,5-bis(fluoranyl)-~{N}-[3-[(2-fluoranyl-4-methoxy-phenyl)sulfamoyl]phenyl]benzamide


Mass: 436.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H15F3N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.59 Å3/Da / Density % sol: 52.58 % / Mosaicity: 0.26 °
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: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 1.88→47.69 Å / Num. obs: 53637 / % possible obs: 99.4 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.027 / Rrim(I) all: 0.094 / Net I/σ(I): 19.4 / Num. measured all: 593811 / Scaling rejects: 10
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.968 / Num. measured all: 23506 / Num. unique obs: 3114 / CC1/2: 0.585 / Rpim(I) all: 0.345 / Rrim(I) all: 1.034 / Net I/σ(I) obs: 1.9 / % possible all: 91.9

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Processing

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

6w29


Resolution: 1.88→45.96 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.427 / SU ML: 0.097 / SU R Cruickshank DPI: 0.1406 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.129
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 2607 4.9 %RANDOM
Rwork0.1931 ---
obs0.1945 50910 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.41 Å2 / Biso mean: 27.653 Å2 / Biso min: 15.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0 Å2
2--0.09 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: final / Resolution: 1.88→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4257 0 58 339 4654
Biso mean--40.07 33.14 -
Num. residues----544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134408
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174158
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.6535981
X-RAY DIFFRACTIONr_angle_other_deg1.3991.5779632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5185545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12222.063223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80315752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9871530
X-RAY DIFFRACTIONr_chiral_restr0.1340.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024909
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02917
LS refinement shellResolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 170 -
Rwork0.296 3426 -
all-3596 -
obs--91.92 %

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