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- PDB-5i7n: MaoC-like dehydratase -

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Basic information

Entry
Database: PDB / ID: 5i7n
TitleMaoC-like dehydratase
ComponentsMaoC-like dehydratase
KeywordsLYASE / enzyme / hydratase / MaoC like
Function / homology: / N-terminal of MaoC-like dehydratase / FAS1-like, dehydratase domain region / MaoC-like dehydratase domain / MaoC like domain / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / HotDog domain superfamily / fatty acid biosynthetic process / MaoC-like dehydratase
Function and homology information
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBlaise, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Deletion of a dehydratase important for intracellular growth and cording renders rough Mycobacterium abscessus avirulent.
Authors: Halloum, I. / Carrere-Kremer, S. / Blaise, M. / Viljoen, A. / Bernut, A. / Le Moigne, V. / Vilcheze, C. / Guerardel, Y. / Lutfalla, G. / Herrmann, J.L. / Jacobs, W.R. / Kremer, L.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Aug 3, 2016Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MaoC-like dehydratase


Theoretical massNumber of molelcules
Total (without water)36,6721
Polymers36,6721
Non-polymers00
Water9,602533
1
A: MaoC-like dehydratase

A: MaoC-like dehydratase


Theoretical massNumber of molelcules
Total (without water)73,3442
Polymers73,3442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3220 Å2
ΔGint-8 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.320, 83.320, 124.390
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-667-

HOH

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Components

#1: Protein MaoC-like dehydratase


Mass: 36672.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Gene: MAB_4780 / Plasmid: pET-32 ek/lic / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): rosetta 2 pLys / References: UniProt: B1MM63
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH8.5, 2.8 M AmSO4, 1mM trans-2-dodecanoyl-CoA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 52624 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.5
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 6.58 % / Mean I/σ(I) obs: 2.12 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4v12

4v12


Resolution: 1.65→42.772 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.71
RfactorNum. reflection% reflection
Rfree0.1906 2000 3.8 %
Rwork0.1614 --
obs0.1625 52613 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→42.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 0 0 533 2997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062628
X-RAY DIFFRACTIONf_angle_d0.7613587
X-RAY DIFFRACTIONf_dihedral_angle_d13.781958
X-RAY DIFFRACTIONf_chiral_restr0.081405
X-RAY DIFFRACTIONf_plane_restr0.005474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6499-1.69120.27561380.23243501X-RAY DIFFRACTION98
1.6912-1.73690.21971410.21083550X-RAY DIFFRACTION98
1.7369-1.7880.25271380.2073514X-RAY DIFFRACTION98
1.788-1.84570.231400.20093550X-RAY DIFFRACTION98
1.8457-1.91170.2141400.18693531X-RAY DIFFRACTION98
1.9117-1.98830.21321410.17733567X-RAY DIFFRACTION98
1.9883-2.07870.19941420.16213588X-RAY DIFFRACTION99
2.0787-2.18830.18211420.16173584X-RAY DIFFRACTION99
2.1883-2.32540.21381420.15953607X-RAY DIFFRACTION99
2.3254-2.5050.19261430.15233629X-RAY DIFFRACTION99
2.505-2.7570.17631440.15623648X-RAY DIFFRACTION99
2.757-3.15580.19941460.15583686X-RAY DIFFRACTION100
3.1558-3.97560.17051480.14343742X-RAY DIFFRACTION100
3.9756-42.78660.15961550.14733916X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.61950.15440.90951.44490.47731.0405-0.08320.18080.2266-0.08320.05030.06950.00790.03320.00610.071-0.0141-0.01540.0905-0.00310.0968-5.680117.4373-25.8501
22.24160.07540.46651.19010.08792.0689-0.08930.40720.1575-0.16120.0284-0.2119-0.02580.55720.04940.1129-0.0253-0.0020.25940.02720.14926.243121.3344-30.6473
30.4340.46070.42022.47741.25661.1865-0.0340.42670.1426-0.37340.2566-0.6056-0.29450.5485-0.13910.2924-0.07030.05430.54720.00310.342210.103616.1903-39.4955
41.60190.55260.97180.9611.12912.66360.08720.0315-0.02440.14880.0795-0.13960.22960.2728-0.12490.08630.0255-0.02160.10560.0020.10035.215112.8226-14.7116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 194 )
4X-RAY DIFFRACTION4chain 'A' and (resid 195 through 342 )

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