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- PDB-6au9: Crystal structure of Mycobacterium tuberculosis malate synthase i... -

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Basic information

Entry
Database: PDB / ID: 6au9
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with dioxine-phenyldiketoacid
ComponentsMalate synthase G
KeywordsTRANSFERASE/TRANSFERASE inhibitor / Acetyltransferase / Structural Genomics / TB Structural Genomics Consortium / TBSGC / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / coenzyme A binding / adhesion of symbiont to host / glyoxylate catabolic process / coenzyme A metabolic process / glyoxylate cycle / fibronectin binding ...host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / coenzyme A binding / adhesion of symbiont to host / glyoxylate catabolic process / coenzyme A metabolic process / glyoxylate cycle / fibronectin binding / laminin binding / tricarboxylic acid cycle / peptidoglycan-based cell wall / cell surface / magnesium ion binding / protein homodimerization activity / extracellular region / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Malate synthase G / : / Malate synthase G, alpha-beta insertion domain / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase / Malate synthase superfamily / Malate synthase, C-terminal superfamily / Malate synthase, N-terminal and TIM-barrel domains ...Malate synthase G / : / Malate synthase G, alpha-beta insertion domain / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase / Malate synthase superfamily / Malate synthase, C-terminal superfamily / Malate synthase, N-terminal and TIM-barrel domains / : / : / Malate synthase, TIM barrel domain / Malate synthase, N-terminal domain / Malate synthase, C-terminal / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-BXS / DI(HYDROXYETHYL)ETHER / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKrieger, I.V. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
Citation
Journal: J Chem Inf Model / Year: 2018
Title: Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.
Authors: Ellenbarger, J.F. / Krieger, I.V. / Huang, H.L. / Gomez-Coca, S. / Ioerger, T.R. / Sacchettini, J.C. / Wheeler, S.E. / Dunbar, K.R.
#1: Journal: Chem. Biol. / Year: 2012
Title: Structure-guided discovery of phenyl-diketo acids as potent inhibitors of M. tuberculosis malate synthase.
Authors: Krieger, I.V. / Freundlich, J.S. / Gawandi, V.B. / Roberts, J.P. / Sun, Q. / Owen, J.L. / Fraile, M.T. / Huss, S.I. / Lavandera, J.L. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionAug 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0506
Polymers80,4571
Non-polymers5935
Water8,809489
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.071, 78.071, 223.463
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Malate synthase G


Mass: 80456.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1837c / Production host: Escherichia coli (E. coli)
References: UniProt: A5U3K4, UniProt: P9WK17*PLUS, malate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BXS / (2Z)-4-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-hydroxy-4-oxobut-2-enoic acid


Mass: 250.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.12 Å3/Da / Density % sol: 41.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG3350, MgCl2, TRIS-HCl / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 41626 / % possible obs: 99.9 % / Redundancy: 14 % / Rmerge(I) obs: 0.218 / Net I/σ(I): 7.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 14.4 % / Rmerge(I) obs: 1.439 / Num. unique obs: 2053 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8I

1n8i


Resolution: 2.1→49.493 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.81
RfactorNum. reflection% reflection
Rfree0.199 2024 4.87 %
Rwork0.1629 --
obs0.1648 41541 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5452 0 40 489 5981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075695
X-RAY DIFFRACTIONf_angle_d0.8367751
X-RAY DIFFRACTIONf_dihedral_angle_d9.824680
X-RAY DIFFRACTIONf_chiral_restr0.05882
X-RAY DIFFRACTIONf_plane_restr0.0071020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0956-2.1480.27951170.18382721X-RAY DIFFRACTION98
2.148-2.20610.25631310.18362788X-RAY DIFFRACTION100
2.2061-2.2710.26431440.17992751X-RAY DIFFRACTION100
2.271-2.34430.27431550.17482780X-RAY DIFFRACTION100
2.3443-2.42810.22331200.17622796X-RAY DIFFRACTION100
2.4281-2.52530.23041480.17662781X-RAY DIFFRACTION100
2.5253-2.64020.24581690.16672759X-RAY DIFFRACTION100
2.6402-2.77940.23191500.1662817X-RAY DIFFRACTION100
2.7794-2.95360.22431350.16532803X-RAY DIFFRACTION100
2.9536-3.18160.20821530.17232810X-RAY DIFFRACTION100
3.1816-3.50170.18021510.16082847X-RAY DIFFRACTION100
3.5017-4.00820.17251360.14712861X-RAY DIFFRACTION100
4.0082-5.04910.15261630.1372911X-RAY DIFFRACTION100
5.0491-49.50680.16391520.17123092X-RAY DIFFRACTION100

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