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- PDB-5cbj: Crystal structure of Mycobacterium tuberculosis malate synthase i... -

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Basic information

Entry
Database: PDB / ID: 5cbj
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 3-(phenylthio)acrylic acid
ComponentsMalate synthase G
KeywordsTRANSFERASE / Complex / Fragment
Function / homology
Function and homology information


host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / glyoxylate catabolic process / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic process / glyoxylate cycle / fibronectin binding ...host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / glyoxylate catabolic process / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic process / glyoxylate cycle / fibronectin binding / laminin binding / tricarboxylic acid cycle / peptidoglycan-based cell wall / magnesium ion binding / cell surface / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm / cytosol
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
(2E)-3-(phenylsulfanyl)prop-2-enoic acid / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.957 Å
AuthorsHuang, H.-L. / Sacchettini, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1024055 United States
Citation
Journal: J. Biol. Chem. / Year: 2016
Title: Mycobacterium tuberculosis Malate Synthase Structures with Fragments Reveal a Portal for Substrate/Product Exchange.
Authors: Huang, H.L. / Krieger, I.V. / Parai, M.K. / Gawandi, V.B. / Sacchettini, J.C.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Biochemical and structural studies of malate synthase from Mycobacterium tuberculosis.
Authors: Smith, C.V. / Huang, C.C. / Miczak, A. / Russell, D.G. / Sacchettini, J.C. / Honer zu Bentrup, K.
#2: 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. / Gawandi, V.B. / Sun, Q. / Owen, J.L. / Fraile, M.T. / Huss, S.I. / Lavandera, J.L. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionJun 30, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
A: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6613
Polymers80,4571
Non-polymers2052
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.033, 79.033, 225.862
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 / Mutation: C619A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: glcB, Rv1837c, MTCY1A11.06 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P9WK17, 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-4ZD / (2E)-3-(phenylsulfanyl)prop-2-enoic acid


Mass: 180.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, magnesium chloride, tris / PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.96→44.87 Å / Num. all: 52827 / Num. obs: 46989 / % possible obs: 88.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 34.007 Å2 / Rsym value: 0.0424 / Net I/σ(I): 15.81
Reflection shellResolution: 1.96→2.05 Å / Redundancy: 3.3 % / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8I

1n8i


Resolution: 1.957→44.873 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2719 2404 5.12 %Random selection
Rwork0.208 ---
obs0.2113 46965 89.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.957→44.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5421 0 13 535 5969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075534
X-RAY DIFFRACTIONf_angle_d1.0947520
X-RAY DIFFRACTIONf_dihedral_angle_d14.5062015
X-RAY DIFFRACTIONf_chiral_restr0.076857
X-RAY DIFFRACTIONf_plane_restr0.005992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9567-1.99660.32151510.27612488X-RAY DIFFRACTION86
1.9966-2.040.34161530.25432750X-RAY DIFFRACTION96
2.04-2.08750.35471460.25082801X-RAY DIFFRACTION97
2.0875-2.13970.31991850.24442743X-RAY DIFFRACTION96
2.1397-2.19750.32281410.23482776X-RAY DIFFRACTION96
2.1975-2.26220.31161530.23172742X-RAY DIFFRACTION95
2.2622-2.33520.3151470.22442751X-RAY DIFFRACTION95
2.3352-2.41870.29661590.21612713X-RAY DIFFRACTION94
2.4187-2.51550.28441250.20592707X-RAY DIFFRACTION93
2.5155-2.630.28741220.20222737X-RAY DIFFRACTION92
2.63-2.76860.29421470.20932655X-RAY DIFFRACTION92
2.7686-2.94210.25841370.20572709X-RAY DIFFRACTION91
2.9421-3.16920.24541400.20382688X-RAY DIFFRACTION91
3.1692-3.4880.28381500.2022555X-RAY DIFFRACTION87
3.488-3.99240.26671240.19972281X-RAY DIFFRACTION76
3.9924-5.0290.22641120.19062012X-RAY DIFFRACTION67
5.029-44.88520.23211120.19442453X-RAY DIFFRACTION75

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