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- PDB-4v12: Crystal structure of the MSMEG_6754 dehydratase from Mycobacteriu... -

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Basic information

Entry
Database: PDB / ID: 4v12
TitleCrystal structure of the MSMEG_6754 dehydratase from Mycobacterium smegmatis
ComponentsMAOC LIKE DOMAIN PROTEIN
KeywordsOXIDOREDUCTASE
Function / homologyN-terminal of MaoC-like dehydratase / FAS1-like, dehydratase domain region / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / Chem-POG / MaoC like domain protein
Function and homology information
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsBlaise, M.
CitationJournal: Mol.Microbiol. / Year: 2015
Title: A New Dehydratase Conferring Innate Resistance to Thiacetazone and Intra-Amoebal Survival of Mycobacterium Smegmatis.
Authors: Carrere-Kremer, S. / Blaise, M. / Singh, V.K. / Alibaud, L. / Tuaillon, E. / Halloum, I. / Van De Weerd, R. / Guerardel, Y. / Drancourt, M. / Takiff, H. / Geurtsen, J. / Kremer, L.
History
DepositionSep 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: MAOC LIKE DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6563
Polymers37,0231
Non-polymers6342
Water5,513306
1
A: MAOC LIKE DOMAIN PROTEIN
hetero molecules

A: MAOC LIKE DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3136
Polymers74,0452
Non-polymers1,2684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5340 Å2
ΔGint-13.2 kcal/mol
Surface area27500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.390, 84.390, 122.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2108-

HOH

21A-2304-

HOH

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Components

#1: Protein MAOC LIKE DOMAIN PROTEIN


Mass: 37022.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Plasmid: PET32 EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: A0R724
#2: Chemical ChemComp-POG / (20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL / POLYPROPYLENE GLYCOL / HEPTAPROPYLENE GLYCOL


Mass: 424.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44O8
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ADDITIONAL GLYCINE IN N-TERMINUS COMES FROM THE LEFT OVER OF TEV CLEAVAGE SITE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.11 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS PH 6.5, 45% V/V POLYPROPYLENE GLYCOL P 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 70527 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 16.37 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.8
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.2 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.5→29.297 Å / SU ML: 0.12 / σ(F): 1.99 / Phase error: 15.87 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1776 2000 2.8 %
Rwork0.1591 --
obs0.1596 70488 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 27 306 2898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092761
X-RAY DIFFRACTIONf_angle_d1.1613779
X-RAY DIFFRACTIONf_dihedral_angle_d12.1331008
X-RAY DIFFRACTIONf_chiral_restr0.051433
X-RAY DIFFRACTIONf_plane_restr0.006502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.2861380.25634737X-RAY DIFFRACTION98
1.5375-1.57910.22521410.21124790X-RAY DIFFRACTION99
1.5791-1.62560.18611410.18894854X-RAY DIFFRACTION100
1.6256-1.6780.23431420.17174860X-RAY DIFFRACTION100
1.678-1.7380.19051420.16344844X-RAY DIFFRACTION100
1.738-1.80760.18491430.16034911X-RAY DIFFRACTION100
1.8076-1.88980.17811420.15754885X-RAY DIFFRACTION100
1.8898-1.98940.20161430.1564898X-RAY DIFFRACTION100
1.9894-2.11410.16771440.15184904X-RAY DIFFRACTION100
2.1141-2.27720.17171420.14854892X-RAY DIFFRACTION100
2.2772-2.50630.16851440.15674923X-RAY DIFFRACTION99
2.5063-2.86870.17351440.164940X-RAY DIFFRACTION99
2.8687-3.61320.18551450.15944965X-RAY DIFFRACTION99
3.6132-29.30280.15011490.14575085X-RAY DIFFRACTION96

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