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- PDB-5jbw: Crystal structure of LiuC -

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Basic information

Entry
Database: PDB / ID: 5jbw
TitleCrystal structure of LiuC
Components3-hydroxybutyryl-CoA dehydratase
KeywordsLYASE / Dehydratase / isovalerate / Myxococcus xanthus
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydratase / lyase activity
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-hydroxybutyryl-CoA dehydratase
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBock, T. / Reichelt, J. / Mueller, R. / Blankenfeldt, W.
CitationJournal: Chembiochem / Year: 2016
Title: The Structure of LiuC, a 3-Hydroxy-3-Methylglutaconyl CoA Dehydratase Involved in Isovaleryl-CoA Biosynthesis in Myxococcus xanthus, Reveals Insights into Specificity and Catalysis.
Authors: Bock, T. / Reichelt, J. / Muller, R. / Blankenfeldt, W.
History
DepositionApr 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxybutyryl-CoA dehydratase


Theoretical massNumber of molelcules
Total (without water)27,6341
Polymers27,6341
Non-polymers00
Water5,188288
1
A: 3-hydroxybutyryl-CoA dehydratase

A: 3-hydroxybutyryl-CoA dehydratase

A: 3-hydroxybutyryl-CoA dehydratase


Theoretical massNumber of molelcules
Total (without water)82,9013
Polymers82,9013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10020 Å2
ΔGint-52 kcal/mol
Surface area29780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.790, 115.790, 115.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-512-

HOH

31A-585-

HOH

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Components

#1: Protein 3-hydroxybutyryl-CoA dehydratase


Mass: 27633.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Gene: crt, MXAN_3757 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1D5Y4, 3-hydroxybutyryl-CoA dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 4.68 Å3/Da / Density % sol: 73.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M TRIS-HCl pH 8.5, 0.2 M MgCl2 and 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.05→40.94 Å / Num. obs: 32751 / % possible obs: 100 % / Redundancy: 23.4 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.189 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.05-2.1123.11.5421100
8.94-40.9419.40.056199.1

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Processing

Software
NameVersionClassification
Aimless0.5.24data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQF

3kqf


Resolution: 2.05→40.938 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.65
RfactorNum. reflection% reflection
Rfree0.2098 1657 5.06 %
Rwork0.1733 --
obs0.1751 32722 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.18 Å2 / Biso mean: 34.4094 Å2 / Biso min: 19.06 Å2
Refinement stepCycle: final / Resolution: 2.05→40.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 0 288 2212
Biso mean---40.09 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011955
X-RAY DIFFRACTIONf_angle_d0.9692641
X-RAY DIFFRACTIONf_chiral_restr0.058308
X-RAY DIFFRACTIONf_plane_restr0.006350
X-RAY DIFFRACTIONf_dihedral_angle_d141201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0501-2.11040.27181240.217725832707
2.1104-2.17850.21241450.204225852730
2.1785-2.25640.22441570.182625082665
2.2564-2.34670.19831420.167325582700
2.3467-2.45350.20531420.153625452687
2.4535-2.58290.17041340.154125752709
2.5829-2.74470.17771340.157525992733
2.7447-2.95650.21131430.170225602703
2.9565-3.25390.20511120.171426052717
3.2539-3.72450.21411500.169425962746
3.7245-4.69140.17761310.154926392770
4.6914-40.94610.25591430.199127122855

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