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- PDB-3sad: Crystal structure of Mycobacterium tuberculosis malate synthase i... -

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Basic information

Entry
Database: PDB / ID: 3sad
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in complex with 4-(2-mehtylphenyl)-2,4-dioxobutanoic acid inhibitor
ComponentsMalate synthase G
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / inhibitor complex / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / malate synthase / 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 / manganese ion binding / cell surface / magnesium ion binding / protein homodimerization activity / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Malate synthase G - maily-beta sub-domain / Malate synthase G - maily-beta sub-domain / 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 G - maily-beta sub-domain / Malate synthase G - maily-beta sub-domain / 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 / Beta Complex / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-(2-methylphenyl)-2,4-dioxobutanoic acid / Malate synthase G / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.82 Å
AuthorsKrieger, I.V. / Sun, Q. / Sacchettini, J.C. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: 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
DepositionJun 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)80,7365
Polymers80,4571
Non-polymers2794
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.737, 77.737, 221.986
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) / Gene: glcB, Rv1837c, MT1885, MTCY1A11.06 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5J4, 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-040 / 4-(2-methylphenyl)-2,4-dioxobutanoic acid


Mass: 206.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDEVIATIONS FROM SP2 GEOMETRY POTENTIALLY ARE DUE TO CHARGE INFLUENCING INTERACTIONS WITH THE PROTEIN.

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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: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 0.1 M magnesium chloride, 0.1 M TRIS-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2008
RadiationMonochromator: double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.62→44.13 Å / Num. all: 87314 / Num. obs: 87314 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Net I/σ(I): 6.4
Reflection shellResolution: 1.62→1.68 Å / % possible all: 25.3

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
REFMACrefinement
PHENIXmodel building
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
PHENIXphasing
HKL-2000data collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1N8I

1n8i


Resolution: 1.82→44.125 Å / Cor.coef. Fo:Fc: 0.9545 / Cor.coef. Fo:Fc free: 0.9386 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 3148 5.08 %
Rwork0.1704 --
obs0.1729 62029 99.98 %
all-87314 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.851 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0996 Å2-0 Å20 Å2
2---3.0996 Å20 Å2
3---6.1993 Å2
Refine analyzeLuzzati coordinate error obs: 0.189 Å
Refinement stepCycle: LAST / Resolution: 1.82→44.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5431 0 18 641 6090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075700
X-RAY DIFFRACTIONf_angle_d1.0137781
X-RAY DIFFRACTIONf_dihedral_angle_d14.0242137
X-RAY DIFFRACTIONf_chiral_restr0.069892
X-RAY DIFFRACTIONf_plane_restr0.0081027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.84840.28671450.21212623X-RAY DIFFRACTION100
1.8484-1.87870.28991330.2142600X-RAY DIFFRACTION100
1.8787-1.91110.27441310.21012659X-RAY DIFFRACTION100
1.9111-1.94590.26021410.19552632X-RAY DIFFRACTION100
1.9459-1.98330.2491520.18852620X-RAY DIFFRACTION100
1.9833-2.02380.24911500.18782609X-RAY DIFFRACTION100
2.0238-2.06780.25691390.18592648X-RAY DIFFRACTION100
2.0678-2.11590.23761380.17842661X-RAY DIFFRACTION100
2.1159-2.16880.23821510.17372631X-RAY DIFFRACTION100
2.1688-2.22750.2111520.17862628X-RAY DIFFRACTION100
2.2275-2.2930.24451340.16572676X-RAY DIFFRACTION100
2.293-2.3670.23641370.17762631X-RAY DIFFRACTION100
2.367-2.45160.24131360.17652678X-RAY DIFFRACTION100
2.4516-2.54980.20821390.17022648X-RAY DIFFRACTION100
2.5498-2.66580.23551550.17362675X-RAY DIFFRACTION100
2.6658-2.80630.25961490.18572671X-RAY DIFFRACTION100
2.8063-2.98210.22461370.17472703X-RAY DIFFRACTION100
2.9821-3.21230.21561240.17282704X-RAY DIFFRACTION100
3.2123-3.53540.20381570.15682709X-RAY DIFFRACTION100
3.5354-4.04670.19171460.14532737X-RAY DIFFRACTION100
4.0467-5.09720.15221420.14132788X-RAY DIFFRACTION100
5.0972-44.13840.21111600.17452950X-RAY DIFFRACTION100

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