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

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Basic information

Entry
Database: PDB / ID: 6dko
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 2,6-F-phenyldiketoacid
ComponentsMalate synthase G
KeywordsLYASE/LYASE inhibitor / Acetyltransferase / Structural Genomics / TB Structural Genomics Consortium / TBSGC / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex / PSI-2 / Protein Structure Initiative / LYASE / LYASE-LYASE 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 / 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
4-(2,6-difluorophenyl)-2,4-dioxobutanoic acid / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.556 Å
AuthorsKrieger, I.V. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)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
DepositionMay 30, 2018Deposition 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 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _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)80,7585
Polymers80,4571
Non-polymers3014
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-11 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.016, 79.016, 225.961
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: glcB / Production host: Escherichia coli (E. coli)
References: UniProt: A0A045ITM4, 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-GXG / 4-(2,6-difluorophenyl)-2,4-dioxobutanoic acid


Mass: 228.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6F2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, 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: 19-ID / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 100848 / % possible obs: 97.6 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 7
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 3913 / % possible all: 76.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8I

1n8i


Resolution: 1.556→37.294 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.59
RfactorNum. reflection% reflection
Rfree0.2228 4875 4.89 %
Rwork0.1928 --
obs0.1942 99671 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.556→37.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5475 0 19 530 6024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065683
X-RAY DIFFRACTIONf_angle_d0.8477743
X-RAY DIFFRACTIONf_dihedral_angle_d10.5984667
X-RAY DIFFRACTIONf_chiral_restr0.053883
X-RAY DIFFRACTIONf_plane_restr0.0061024
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5562-1.57390.36711080.34711895X-RAY DIFFRACTION59
1.5739-1.59240.35821210.32812325X-RAY DIFFRACTION73
1.5924-1.61180.31421520.31882659X-RAY DIFFRACTION82
1.6118-1.63220.34481420.30692894X-RAY DIFFRACTION91
1.6322-1.65370.31771680.29723030X-RAY DIFFRACTION94
1.6537-1.67640.32491620.28683149X-RAY DIFFRACTION97
1.6764-1.70030.30131610.26813197X-RAY DIFFRACTION99
1.7003-1.72570.30531500.25913256X-RAY DIFFRACTION100
1.7257-1.75270.27941510.25623245X-RAY DIFFRACTION100
1.7527-1.78140.27991590.24963234X-RAY DIFFRACTION100
1.7814-1.81210.29821500.26923252X-RAY DIFFRACTION100
1.8121-1.84510.27441460.24423238X-RAY DIFFRACTION100
1.8451-1.88060.26241810.23853287X-RAY DIFFRACTION100
1.8806-1.91890.27291590.22653222X-RAY DIFFRACTION100
1.9189-1.96070.27871820.22073243X-RAY DIFFRACTION100
1.9607-2.00630.27151750.22013245X-RAY DIFFRACTION100
2.0063-2.05640.24281850.21343218X-RAY DIFFRACTION100
2.0564-2.1120.27981680.21753261X-RAY DIFFRACTION100
2.112-2.17420.25971620.21213277X-RAY DIFFRACTION100
2.1742-2.24430.25721600.21073285X-RAY DIFFRACTION100
2.2443-2.32450.23821520.19623301X-RAY DIFFRACTION100
2.3245-2.41760.23981740.19723242X-RAY DIFFRACTION100
2.4176-2.52760.21791830.19643278X-RAY DIFFRACTION100
2.5276-2.66080.25591680.19253306X-RAY DIFFRACTION100
2.6608-2.82750.20041700.19743295X-RAY DIFFRACTION100
2.8275-3.04570.22571790.19783317X-RAY DIFFRACTION100
3.0457-3.3520.23651900.193294X-RAY DIFFRACTION100
3.352-3.83660.19481710.17353362X-RAY DIFFRACTION100
3.8366-4.83210.17031680.14543400X-RAY DIFFRACTION99
4.8321-37.30430.17081780.16443589X-RAY DIFFRACTION99

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