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- PDB-6c8p: Crystal structure of Mycobacterium tuberculosis malate synthase i... -

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Basic information

Entry
Database: PDB / ID: 6c8p
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 2-F-phenyldiketoacid
ComponentsMalate synthase G
KeywordsTRANSFERASE / Acetyltransferase / Structural Genomics / 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 / 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 / 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-EQA / DI(HYDROXYETHYL)ETHER / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.635 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
DepositionJan 25, 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 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 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)80,8466
Polymers80,4571
Non-polymers3895
Water9,494527
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)78.772, 78.772, 224.698
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: A5U3K4, 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-EQA / (2Z)-4-(2-fluorophenyl)-2-hydroxy-4-oxobut-2-enoic acid


Mass: 210.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H7FO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: TRIS-HCl, MgCl2, PEG3350 / 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: 1.635→74.34 Å / Num. obs: 88365 / % possible obs: 84.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.2
Reflection shellResolution: 1.62→1.635 Å / Rmerge(I) obs: 1.236

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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: 1.635→44.696 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.64
RfactorNum. reflection% reflection
Rfree0.2171 3746 4.99 %
Rwork0.1865 --
obs0.1881 75001 84.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.635→44.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 25 527 6024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075653
X-RAY DIFFRACTIONf_angle_d0.8567698
X-RAY DIFFRACTIONf_dihedral_angle_d10.744660
X-RAY DIFFRACTIONf_chiral_restr0.054879
X-RAY DIFFRACTIONf_plane_restr0.0061017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6353-1.6560.6316200.541445X-RAY DIFFRACTION15
1.656-1.67780.4531340.5303586X-RAY DIFFRACTION19
1.6778-1.70080.4521440.40321176X-RAY DIFFRACTION38
1.7008-1.72510.3579830.36311535X-RAY DIFFRACTION50
1.7251-1.75090.32621030.33091943X-RAY DIFFRACTION63
1.7509-1.77820.33771160.32092075X-RAY DIFFRACTION69
1.7782-1.80740.36451380.30682398X-RAY DIFFRACTION79
1.8074-1.83850.3191420.28562655X-RAY DIFFRACTION87
1.8385-1.8720.33611530.27212940X-RAY DIFFRACTION95
1.872-1.9080.30691490.25572974X-RAY DIFFRACTION97
1.908-1.94690.26181440.24963057X-RAY DIFFRACTION99
1.9469-1.98930.29021810.24433015X-RAY DIFFRACTION98
1.9893-2.03550.23981400.22283008X-RAY DIFFRACTION98
2.0355-2.08640.2661640.21393037X-RAY DIFFRACTION99
2.0864-2.14290.2371590.2013085X-RAY DIFFRACTION99
2.1429-2.20590.25021510.19383032X-RAY DIFFRACTION99
2.2059-2.27710.23581650.19233033X-RAY DIFFRACTION99
2.2771-2.35850.27761670.18423045X-RAY DIFFRACTION99
2.3585-2.45290.24121540.19463101X-RAY DIFFRACTION99
2.4529-2.56450.21111390.19083085X-RAY DIFFRACTION99
2.5645-2.69970.27761560.19393090X-RAY DIFFRACTION99
2.6997-2.86890.20611700.19213080X-RAY DIFFRACTION99
2.8689-3.09030.21651810.18873118X-RAY DIFFRACTION99
3.0903-3.40120.1971730.18223108X-RAY DIFFRACTION99
3.4012-3.89310.18961670.16083109X-RAY DIFFRACTION98
3.8931-4.90390.17531800.14283150X-RAY DIFFRACTION97
4.9039-44.71230.17961730.16593375X-RAY DIFFRACTION98

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