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- PDB-2c27: The Structure of Mycothiol Synthase in Complex with des- AcetylMy... -

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Basic information

Entry
Database: PDB / ID: 2c27
TitleThe Structure of Mycothiol Synthase in Complex with des- AcetylMycothiol and CoenzymeA.
ComponentsMYCOTHIOL SYNTHASE
KeywordsSYNTHASE / MYCOBACTERIUM TUBERCULOSIS / MYCOTHIOL SYNTHASE / DES- ACETYLMYCOTHIOL / ACETYLTRANSFERASE / GNAT / GCN5 RELATED N- ACETYLTRANSFERASE
Function / homology
Function and homology information


mycothiol synthase / mycothiol metabolic process / mycothiol synthase activity / N-terminal peptidyl-alanine acetylation / Mycothiol biosynthesis / mycothiol biosynthetic process / peptide-alanine-alpha-N-acetyltransferase activity / biological process involved in interaction with host / cellular response to acidic pH / acyltransferase activity, transferring groups other than amino-acyl groups ...mycothiol synthase / mycothiol metabolic process / mycothiol synthase activity / N-terminal peptidyl-alanine acetylation / Mycothiol biosynthesis / mycothiol biosynthetic process / peptide-alanine-alpha-N-acetyltransferase activity / biological process involved in interaction with host / cellular response to acidic pH / acyltransferase activity, transferring groups other than amino-acyl groups / cellular response to hydrogen peroxide / cytosol
Similarity search - Function
Mycothiol acetyltransferase / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / COENZYME A / Chem-MA8 / Mycothiol acetyltransferase / Mycothiol acetyltransferase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVetting, M.W. / Yu, M. / Rendle, P.M. / Blanchard, J.S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Substrate-Induced Conformational Change of Mycobacterium Tuberculosis Mycothiol Synthase.
Authors: Vetting, M.W. / Yu, M. / Rendle, P.M. / Blanchard, J.S.
History
DepositionSep 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.page_last / _struct.title
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYCOTHIOL SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6614
Polymers33,6391
Non-polymers2,0223
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.830, 59.620, 61.670
Angle α, β, γ (deg.)90.00, 91.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MYCOTHIOL SYNTHASE


Mass: 33639.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O53831, UniProt: P9WJM7*PLUS
#2: Sugar ChemComp-MA8 / (1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl 2-(L-cysteinylamino)-2-deoxy-alpha-D-glucopyranoside / (2S,3R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-(L-CYSTEINYLAMINO)-2-DEOXY-ALPHA-L-GLUCOPYRANOSIDE / (1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl 2-(L-cysteinylamino)-2-deoxy-alpha-D-glucoside / (1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl 2-(L-cysteinylamino)-2-deoxy-D-glucoside / (1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl 2-(L-cysteinylamino)-2-deoxy-glucoside


Type: D-saccharide / Mass: 444.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28N2O11S
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDES-ACETYLMYCOTHIOL AND COENZYMEA ARE LINKED BY A DISULFIDE BOND

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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: 1.93 Å3/Da / Density % sol: 35.67 %
Crystal growpH: 8.5
Details: 1 M NA3CITRATE PH 8.5 100 MM BICINE PH 8.8 7.7 MM DESACETYL-MYCOTHIOL 5.3 MM COENZYMEA 40 MM DTT

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Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS-IV / Detector: IMAGE PLATE / Details: OSMIC CONFOCAL MAXFLUX OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 24682 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 7.6 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OZP

1ozp


Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1193 5 %RANDOM
Rwork0.161 ---
obs0.161 24682 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.7512 Å2 / ksol: 0.407886 e/Å3
Displacement parametersBiso mean: 23.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.594 Å20 Å2-0.012 Å2
2--4.229 Å20 Å2
3----1.635 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 106 175 2555
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.91
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.245 5 %
Rwork0.186 -
obs-94.3 %

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