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- PDB-6bu1: Crystal structure of Mycobacterium tuberculosis malate synthase i... -

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Basic information

Entry
Database: PDB / ID: 6bu1
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-Br-3-OH-phenyldiketoacid
ComponentsMalate synthase G
KeywordsSTRUCTURAL GENOMICS / Transferase / Acetyltransferase / TB Structural Genomics Consortium / TBSGC / TRANSFERASE-TRANSFERASE inhibitor complex
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 cycle / glyoxylate catabolic process / 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 cycle / glyoxylate catabolic process / fibronectin binding / laminin binding / tricarboxylic acid cycle / peptidoglycan-based cell wall / cell surface / magnesium ion binding / protein homodimerization activity / extracellular region / plasma membrane / cytoplasm / cytosol
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-E9S / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.584 Å
AuthorsKrieger, I.V. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
Citation
Journal: J Chem Inf Model / Year: 2018
Title: Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.
Authors: Ellenbarger, J.F. / Krieger, I.V. / Huang, H.L. / Gomez-Coca, S. / Ioerger, T.R. / Sacchettini, J.C. / Wheeler, S.E. / Dunbar, K.R.
#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.
History
DepositionDec 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)80,8416
Polymers80,4571
Non-polymers3845
Water12,106672
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)79.538, 79.538, 226.160
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) / Production host: Escherichia coli (E. coli)
References: UniProt: A5U3K4, UniProt: P9WK17*PLUS, 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-E9S / (2Z)-4-(2-bromo-3-hydroxyphenyl)-2-hydroxy-4-oxobut-2-enoic acid


Mass: 287.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7BrO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Tris-HCl, MgCl2 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.584→50 Å / Num. obs: 88699 / % possible obs: 91.3 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 7.9
Reflection shellResolution: 1.584→1.62 Å / Redundancy: 3.8 % / Rmerge(I) obs: 3.011 / Num. unique obs: 2728 / % possible all: 55.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8I

1n8i


Resolution: 1.584→45.079 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.22
RfactorNum. reflection% reflection
Rfree0.2281 4444 5.01 %
Rwork0.1889 --
obs0.1909 88617 89.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.584→45.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5445 0 20 672 6137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075687
X-RAY DIFFRACTIONf_angle_d0.8257760
X-RAY DIFFRACTIONf_dihedral_angle_d10.8914677
X-RAY DIFFRACTIONf_chiral_restr0.052884
X-RAY DIFFRACTIONf_plane_restr0.0061028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5842-1.60220.5189350.4392781X-RAY DIFFRACTION25
1.6022-1.62110.439590.38481423X-RAY DIFFRACTION46
1.6211-1.64080.3917890.38831723X-RAY DIFFRACTION56
1.6408-1.66160.3744760.381948X-RAY DIFFRACTION62
1.6616-1.68350.45161240.3632030X-RAY DIFFRACTION66
1.6835-1.70650.37221200.34512222X-RAY DIFFRACTION71
1.7065-1.73090.39221360.33832365X-RAY DIFFRACTION76
1.7309-1.75670.35841260.33292619X-RAY DIFFRACTION84
1.7567-1.78420.38031650.31042820X-RAY DIFFRACTION91
1.7842-1.81340.31431530.28893074X-RAY DIFFRACTION98
1.8134-1.84470.31241670.27093083X-RAY DIFFRACTION99
1.8447-1.87830.33221650.25733071X-RAY DIFFRACTION100
1.8783-1.91440.30021600.24843105X-RAY DIFFRACTION99
1.9144-1.95350.26171600.23553114X-RAY DIFFRACTION100
1.9535-1.99590.27511610.22783110X-RAY DIFFRACTION100
1.9959-2.04240.26151730.22913142X-RAY DIFFRACTION100
2.0424-2.09340.27681690.21293107X-RAY DIFFRACTION100
2.0934-2.15010.22931640.20123125X-RAY DIFFRACTION100
2.1501-2.21330.23181790.18173118X-RAY DIFFRACTION100
2.2133-2.28480.26051840.1943111X-RAY DIFFRACTION100
2.2848-2.36640.22931700.19073114X-RAY DIFFRACTION100
2.3664-2.46110.23511730.18723151X-RAY DIFFRACTION100
2.4611-2.57320.25411720.19163164X-RAY DIFFRACTION100
2.5732-2.70880.2171560.1943162X-RAY DIFFRACTION100
2.7088-2.87850.22021650.18973185X-RAY DIFFRACTION100
2.8785-3.10070.22151630.1853182X-RAY DIFFRACTION100
3.1007-3.41260.24391620.1843222X-RAY DIFFRACTION100
3.4126-3.90620.22171670.15923228X-RAY DIFFRACTION100
3.9062-4.92040.16481860.13923269X-RAY DIFFRACTION100
4.9204-45.09720.17781650.16623405X-RAY DIFFRACTION97

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