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- PDB-6w29: Trypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC013) -

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Basic information

Entry
Database: PDB / ID: 6w29
TitleTrypanosoma cruzi Malic Enzyme in complex with inhibitor (MEC013)
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 oxidoreductase / Malic enzyme, conserved site / Malic enzymes signature. / 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 oxidoreductase / Malic enzyme, conserved site / Malic enzymes signature. / 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-SEV / Malic enzyme
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 5, 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)62,5375
Polymers61,6101
Non-polymers9274
Water1,33374
1
A: Malic enzyme
hetero molecules

A: Malic enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,07510
Polymers123,2212
Non-polymers1,8548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area4580 Å2
ΔGint-5 kcal/mol
Surface area44470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.519, 73.519, 233.713
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 78 molecules

#2: Chemical ChemComp-SEV / 3,5-bis(fluoranyl)-~{N}-[3-[(4-methoxyphenyl)sulfamoyl]phenyl]benzamide


Mass: 418.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16F2N2O4S / 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: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 1.2-1.4 M Na3-Citrate / PH range: 6.8 -7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.14→47.54 Å / Num. obs: 36499 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.04 / Rrim(I) all: 0.136 / Net I/σ(I): 13
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.054 / Num. measured all: 13953 / Num. unique obs: 2879 / CC1/2: 0.53 / Rpim(I) all: 0.509 / Rrim(I) all: 1.18 / Net I/σ(I) obs: 1.3 / % possible all: 98.8

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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: 1GZ3, 3WJA, 1GQ2

1gz3

3wja

1gq2


Resolution: 2.14→47.54 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.534 / SU ML: 0.157 / SU R Cruickshank DPI: 0.2287 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.186
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1840 5.1 %RANDOM
Rwork0.2059 ---
obs0.2076 34556 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 126.97 Å2 / Biso mean: 40.258 Å2 / Biso min: 23.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å2-0 Å2-0 Å2
2--1.45 Å2-0 Å2
3----2.9 Å2
Refinement stepCycle: final / Resolution: 2.14→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 61 74 4403
Biso mean--64.85 37.33 -
Num. residues----545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134415
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174170
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.6535987
X-RAY DIFFRACTIONr_angle_other_deg1.3231.5779654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7325544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71421.956225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47715752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9151531
X-RAY DIFFRACTIONr_chiral_restr0.080.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02923
LS refinement shellResolution: 2.14→2.196 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 129 -
Rwork0.344 2458 -
all-2587 -
obs--98.37 %

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