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

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Basic information

Entry
Database: PDB / ID: 5drc
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-hydroxy-4-(1H-indol-3-yl)-4-oxobut-2-enoic acid
ComponentsMalate synthase G
KeywordsTRANSFERASE / 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 / coenzyme A metabolic process / glyoxylate catabolic process / glyoxylate cycle / fibronectin binding ...host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / coenzyme A binding / adhesion of symbiont to host / coenzyme A metabolic process / glyoxylate catabolic 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 / cytosol / cytoplasm
Similarity search - Function
: / Malate synthase G, alpha-beta insertion domain / : / : / Malate synthase, N-terminal domain / Malate synthase, C-terminal / Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate synthase, N-terminal and TIM-barrel domains ...: / Malate synthase G, alpha-beta insertion domain / : / : / Malate synthase, N-terminal domain / Malate synthase, C-terminal / Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate synthase, N-terminal and TIM-barrel domains / Malate Synthase G; Chain: A; Domain 4 / Malate synthase, C-terminal superfamily / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5ER / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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
DepositionSep 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 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 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Sep 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_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.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_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.6Nov 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)81,0327
Polymers80,4731
Non-polymers5606
Water9,098505
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.957, 78.957, 224.974
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsMonomer as determined by gel filtration.

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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
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-5ER / (2Z)-2-hydroxy-4-(1H-indol-3-yl)-4-oxobut-2-enoic acid


Mass: 231.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, Tris-HCl, MgCl2 / PH range: 7.0-8.5 / Temp details: Varies between 289-291

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid N2 cryo
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.18→44.783 Å / Num. obs: 33410 / % possible obs: 87.8 % / Redundancy: 6.6 % / Rsym value: 0.0389 / Net I/σ(I): 21.43
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 7.04 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
Blu-IceJBluIce-EPICSdata collection
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8I

1n8i


Resolution: 2.18→44.78 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1669 5 %Random selection
Rwork0.172 ---
obs0.176 33397 87.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5473 0 38 505 6016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075612
X-RAY DIFFRACTIONf_angle_d1.127633
X-RAY DIFFRACTIONf_dihedral_angle_d14.4952041
X-RAY DIFFRACTIONf_chiral_restr0.076868
X-RAY DIFFRACTIONf_plane_restr0.0051006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1823-2.24650.3041390.17482693X-RAY DIFFRACTION92
2.2465-2.31910.25981420.17252757X-RAY DIFFRACTION93
2.3191-2.40190.25071240.1772704X-RAY DIFFRACTION91
2.4019-2.49810.29151520.17752643X-RAY DIFFRACTION90
2.4981-2.61180.31171230.1842624X-RAY DIFFRACTION88
2.6118-2.74950.29991380.1952599X-RAY DIFFRACTION87
2.7495-2.92170.28171350.19562521X-RAY DIFFRACTION84
2.9217-3.14720.27681210.19262495X-RAY DIFFRACTION83
3.1472-3.46380.2741460.18572422X-RAY DIFFRACTION81
3.4638-3.96480.21921210.16542463X-RAY DIFFRACTION81
3.9648-4.99420.22111590.14232645X-RAY DIFFRACTION87
4.9942-44.79220.20461690.16233162X-RAY DIFFRACTION97

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