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- PDB-5h8p: Crystal structure of Mycobacterium tuberculosis malate synthase i... -

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Basic information

Entry
Database: PDB / ID: 5h8p
TitleCrystal structure of Mycobacterium tuberculosis malate synthase in apo form
ComponentsMalate synthase G
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Fragment / 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 / glyoxylate catabolic process / coenzyme A metabolic process / glyoxylate cycle / fibronectin binding ...host cell extracellular matrix binding / capsule / malate synthase / malate synthase activity / coenzyme A binding / adhesion of symbiont to host / glyoxylate catabolic process / 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
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsKrieger, I.V. / Huang, H.-L. / Sacchettini, J.C.
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
DepositionDec 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate synthase G


Theoretical massNumber of molelcules
Total (without water)80,4891
Polymers80,4891
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.792, 81.792, 227.079
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: 80488.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Regions containing residues 1, 73-74, 302-310, 379-381, 676, and 728-741 are disordered and excluded from the final refined model.
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, magnesium chloride, tris / PH range: 7.0-8.5 / Temp details: Varies between 289-291

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.105→45.956 Å / Num. obs: 40305 / % possible obs: 98.2 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.114 / Rsym value: 0.0557 / Net I/σ(I): 11.66
Reflection shellResolution: 2.105→2.14 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 3.21 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
DENZOHKL3000data reduction
SCALEPACKHKL3000data scaling
REFMACCCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8I

1n8i


Resolution: 2.105→45.956 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3122 2052 5.09 %Random selection
Rwork0.2512 ---
obs0.2543 40305 88.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.105→45.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5371 0 0 102 5473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085488
X-RAY DIFFRACTIONf_angle_d1.1637456
X-RAY DIFFRACTIONf_dihedral_angle_d15.9372009
X-RAY DIFFRACTIONf_chiral_restr0.081853
X-RAY DIFFRACTIONf_plane_restr0.005978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1046-2.15360.41791010.33382201X-RAY DIFFRACTION77
2.1536-2.20740.41921570.34632522X-RAY DIFFRACTION94
2.2074-2.26710.4386180.3704333X-RAY DIFFRACTION24
2.2671-2.33380.406900.34911686X-RAY DIFFRACTION98
2.3338-2.40910.41321770.33372842X-RAY DIFFRACTION100
2.4091-2.49520.35611520.32942831X-RAY DIFFRACTION100
2.4952-2.59510.37981460.31072838X-RAY DIFFRACTION100
2.5951-2.71320.3821410.32762875X-RAY DIFFRACTION100
2.7132-2.85620.42641460.31222872X-RAY DIFFRACTION100
2.8562-3.03520.36671460.30722900X-RAY DIFFRACTION100
3.0352-3.26940.38441490.27762873X-RAY DIFFRACTION99
3.2694-3.59830.30971630.24962874X-RAY DIFFRACTION99
3.5983-4.11870.27991520.21442717X-RAY DIFFRACTION93
4.1187-5.18810.22531590.17482906X-RAY DIFFRACTION98
5.1881-45.9670.23841550.19312983X-RAY DIFFRACTION94

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