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

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Basic information

Entry
Database: PDB / ID: 5cjn
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 3-(3-oxo-3,4-dihydroquinoxalin-2-yl)acrylate
ComponentsMalate synthase G
KeywordsTRANSFERASE / Fragment / Complex / Acetyltransferase
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 / 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-52F / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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
DepositionJul 14, 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 ...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_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)80,88510
Polymers80,4731
Non-polymers4139
Water9,872548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-47 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.807, 78.807, 223.823
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: 80472.734 Da / Num. of mol.: 1 / Mutation: C619A
Source method: isolated from a genetically manipulated source
Details: Disordered regions containing residues 71-76, 302-311, 675, 728-741 not included in the final refinement.
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.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-52F / 3-(3-oxo-3,4-dihydroquinoxalin-2-yl)propanoic acid


Mass: 218.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 43.05 %
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: Jun 10, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.186→44.65 Å / Num. obs: 36759 / % possible obs: 97.7 % / Redundancy: 7 % / Biso Wilson estimate: 25.44 Å2 / Rsym value: 0.03 / Net I/σ(I): 26.24
Reflection shellResolution: 2.19→2.3 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 9.76 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPCCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8I

1n8i


Resolution: 2.19→44.65 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1826 4.99 %Random selection
Rwork0.171 ---
obs0.173 36627 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.19→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5439 0 24 548 6011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075567
X-RAY DIFFRACTIONf_angle_d1.0697571
X-RAY DIFFRACTIONf_dihedral_angle_d13.9682027
X-RAY DIFFRACTIONf_chiral_restr0.069863
X-RAY DIFFRACTIONf_plane_restr0.005998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1857-2.24480.24691290.15822510X-RAY DIFFRACTION94
2.2448-2.31090.26151180.16512682X-RAY DIFFRACTION99
2.3109-2.38540.25021350.16182677X-RAY DIFFRACTION99
2.3854-2.47070.2341450.17072674X-RAY DIFFRACTION99
2.4707-2.56960.23671550.16662630X-RAY DIFFRACTION99
2.5696-2.68650.24971380.17082691X-RAY DIFFRACTION99
2.6865-2.82820.24341270.16662712X-RAY DIFFRACTION99
2.8282-3.00530.21091450.16332682X-RAY DIFFRACTION99
3.0053-3.23730.22941390.17162646X-RAY DIFFRACTION97
3.2373-3.56290.22381420.16492612X-RAY DIFFRACTION95
3.5629-4.07820.20941480.15972567X-RAY DIFFRACTION93
4.0782-5.13690.20681630.16052710X-RAY DIFFRACTION97
5.1369-44.65550.24351420.20483008X-RAY DIFFRACTION100

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