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- PDB-5c9u: Crystal structure of Mycobacterium tuberculosis malate synthase i... -

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Basic information

Entry
Database: PDB / ID: 5c9u
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-(2-(2,4-dichlorophenyl)hydrazinyl)-2-oxoacetic acid
ComponentsMalate synthase G
KeywordsTRANSFERASE / Fragment / Complex / acetyl-transferase
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
Chem-4Z1 / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHuang, H.-L. / Sacchettini, J.C.
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: 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.
#2: 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.
History
DepositionJun 29, 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, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)80,7544
Polymers80,4571
Non-polymers2983
Water11,169620
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-12 kcal/mol
Surface area26910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.740, 78.740, 224.655
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 / Plasmid: p6HisF11d / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-4Z1 / [2-(2,4-dichlorophenyl)hydrazinyl](oxo)acetic acid


Mass: 249.051 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6Cl2N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 310 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: 120 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.949→44.681 Å / Num. obs: 49254 / % possible obs: 93.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 18.3

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Processing

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

1n8i


Resolution: 1.95→44.68 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 2514 5.1 %
Rwork0.182 --
obs0.185 49250 93.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5460 0 17 620 6097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095578
X-RAY DIFFRACTIONf_angle_d1.1517585
X-RAY DIFFRACTIONf_dihedral_angle_d13.8592032
X-RAY DIFFRACTIONf_chiral_restr0.082865
X-RAY DIFFRACTIONf_plane_restr0.0061001
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9487-1.98620.27771340.20272609X-RAY DIFFRACTION95
1.9862-2.02680.23281570.19212730X-RAY DIFFRACTION100
2.0268-2.07080.28311510.18432713X-RAY DIFFRACTION100
2.0708-2.1190.25541260.1772716X-RAY DIFFRACTION100
2.119-2.1720.23671470.17732705X-RAY DIFFRACTION100
2.172-2.23070.25131650.17832734X-RAY DIFFRACTION100
2.2307-2.29630.24031470.17712718X-RAY DIFFRACTION100
2.2963-2.37050.23091460.16982736X-RAY DIFFRACTION100
2.3705-2.45520.22751500.17262712X-RAY DIFFRACTION99
2.4552-2.55350.22151360.17292753X-RAY DIFFRACTION99
2.5535-2.66970.2611560.17482703X-RAY DIFFRACTION99
2.6697-2.81040.25221620.18172705X-RAY DIFFRACTION98
2.8104-2.98640.23251430.18492705X-RAY DIFFRACTION97
2.9864-3.2170.25481470.17842650X-RAY DIFFRACTION95
3.217-3.54060.24461280.17892522X-RAY DIFFRACTION90
3.5406-4.05260.22141220.18012166X-RAY DIFFRACTION77
4.0526-5.10470.2011810.17711865X-RAY DIFFRACTION64
5.1047-44.69260.22191160.20552294X-RAY DIFFRACTION75

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