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- PDB-3sb0: Crystal structure of Mycobacterium tuberculosis malate synthase i... -

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Basic information

Entry
Database: PDB / ID: 3sb0
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 4-(2-chloro-6-fluoro-3-methylphenyl)-2,4-dioxobutanoic acid inhibitor
ComponentsMalate synthase G
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / inhibitor complex / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / malate synthase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / manganese ion binding / magnesium ion binding / cell surface / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Malate synthase G - maily-beta sub-domain / Malate synthase G - maily-beta sub-domain / 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 G - maily-beta sub-domain / Malate synthase G - maily-beta sub-domain / 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 / Beta Complex / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-I93 / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.199 Å
AuthorsKrieger, I.V. / Sun, Q. / Sacchettini, J.C. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: 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 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)80,7885
Polymers80,4571
Non-polymers3324
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.534, 78.534, 224.070
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 (bacteria) / Gene: glcB, GlcB (Rv1837c), MT1885, MTCY1A11.06, Rv1837c / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5J4, UniProt: P9WK17*PLUS, malate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-I93 / 4-(2-chloro-6-fluoro-3-methylphenyl)-2,4-dioxobutanoic acid


Mass: 258.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8ClFO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLIGAND I93 WAS BUILD TO MAXIMIZE AGREEMENT WITH THE DENSITY. DEVIATIONS FROM SP2 GEOMETRY ...LIGAND I93 WAS BUILD TO MAXIMIZE AGREEMENT WITH THE DENSITY. DEVIATIONS FROM SP2 GEOMETRY POTENTIALLY ARE DUE TO CHARGE INFLUENCING INTERACTIONS WITH THE PROTEIN.

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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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 0.1 M magnesium chloride, 0.1 M TRIS-HCl , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: 2 x 2 mosaic CCD detector / Detector: CCD / Date: Apr 3, 2010
RadiationMonochromator: double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.73→45.605 Å / Num. all: 71167 / Num. obs: 68086 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.6 % / Rmerge(I) obs: 0.191 / Net I/σ(I): 6.2
Reflection shellResolution: 1.73→1.76 Å / % possible all: 7.5

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
REFMACrefinement
PHENIXmodel building
BUSTER2.8.0refinement
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing
PHENIXphasing
HKL-3000data collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1N8I

1n8i


Resolution: 2.199→45.605 Å / Cor.coef. Fo:Fc: 0.9595 / Cor.coef. Fo:Fc free: 0.9479 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 1825 5 %
Rwork0.1721 --
obs0.1747 36507 99.61 %
all-71167 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.066 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4687 Å20 Å20 Å2
2--0.4687 Å20 Å2
3----0.9375 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: LAST / Resolution: 2.199→45.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 20 400 5838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085548
X-RAY DIFFRACTIONf_angle_d1.0627544
X-RAY DIFFRACTIONf_dihedral_angle_d13.9892032
X-RAY DIFFRACTIONf_chiral_restr0.069860
X-RAY DIFFRACTIONf_plane_restr0.007993
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1993-2.25870.28041280.22322599X-RAY DIFFRACTION99
2.2587-2.32520.29551370.20162606X-RAY DIFFRACTION100
2.3252-2.40020.27181380.1892605X-RAY DIFFRACTION99
2.4002-2.4860.26381480.192607X-RAY DIFFRACTION100
2.486-2.58560.24151440.18642636X-RAY DIFFRACTION100
2.5856-2.70320.25851340.17712639X-RAY DIFFRACTION100
2.7032-2.84570.24491340.17362626X-RAY DIFFRACTION100
2.8457-3.0240.21811480.17712643X-RAY DIFFRACTION100
3.024-3.25740.22731530.17522654X-RAY DIFFRACTION100
3.2574-3.58510.24361360.15462691X-RAY DIFFRACTION100
3.5851-4.10360.17131560.14112682X-RAY DIFFRACTION100
4.1036-5.16890.17511350.13982766X-RAY DIFFRACTION100
5.1689-45.61460.22911340.20282928X-RAY DIFFRACTION100

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