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- PDB-1q7t: Rv1170 (MshB) from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1q7t
TitleRv1170 (MshB) from Mycobacterium tuberculosis
Componentshypothetical protein Rv1170
KeywordsHYDROLASE / modified Rossmann fold / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase / N-acetylglucosaminylinositol deacetylase activity / mycothiol biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / zinc ion binding / plasma membrane
Similarity search - Function
Mycothiol biosynthesis protein, MshB / LmbE-like / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase / 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsMcCarthy, A.A. / Peterson, N.A. / Knijff, R. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure of MshB from Mycobacterium tuberculosis, a Deacetylase Involved in Mycothiol Biosynthesis.
Authors: McCarthy, A.A. / Peterson, N.A. / Knijff, R. / Baker, E.N.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: hypothetical protein Rv1170
B: hypothetical protein Rv1170
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8287
Polymers69,7592
Non-polymers1,0695
Water5,873326
1
A: hypothetical protein Rv1170
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5604
Polymers34,8801
Non-polymers6813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein Rv1170
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2683
Polymers34,8801
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.690, 83.740, 95.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein Rv1170 / MshB / LmbE-related protein


Mass: 34879.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv1170 (MshB) / Plasmid: pProEx-HT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(pRP) / References: UniProt: O50426, UniProt: P9WJN3*PLUS
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: PEG 3000, ammonium sulfate, sodium cacodylate, beta-octylglucoside, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: McCarthy, A.A., (2003) Acta Cryst., D59, 2316.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
124-27 %PEG2000 MME1reservoir
20.2 Mammonium sulfate1reservoir
3100 mMsodium cacodylate1reservoirpH6.1
410 mg/mlprotein1drop
510 mMHEPES1droppH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 46066 / Num. obs: 45788 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.83
Reflection shellHighest resolution: 1.9 Å
Reflection
*PLUS
Num. obs: 44945 / % possible obs: 97.6 % / Num. measured all: 324835 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 94.3 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 7.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→19.35 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2295 5 %RANDOM
Rwork0.19 ---
obs0.19 45788 99.4 %-
all-46066 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.2075 Å2 / ksol: 0.36673 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.11 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 56 326 4866
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.362
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 370 5 %
Rwork0.203 7046 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3BOG.PARAM
X-RAY DIFFRACTION4SULFATE.PARAM
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.214 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73

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