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- PDB-5jbx: Crystal structure of LiuC in complex with coenzyme A and malonic acid -

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Basic information

Entry
Database: PDB / ID: 5jbx
TitleCrystal structure of LiuC in complex with coenzyme A and malonic acid
Components3-hydroxybutyryl-CoA dehydratase
KeywordsLYASE / Dehydratase / isovalerate / Myxococcus xanthus
Function / homology
Function and homology information


3-hydroxybutyryl-CoA dehydratase / fatty acid beta-oxidation / 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
COENZYME A / MALONATE ION / 3-hydroxybutyryl-CoA dehydratase
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: 3-hydroxybutyryl-CoA dehydratase
C: 3-hydroxybutyryl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1369
Polymers83,1933
Non-polymers1,9436
Water20,2851126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint-46 kcal/mol
Surface area28710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.834, 84.773, 128.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-hydroxybutyryl-CoA dehydratase


Mass: 27730.842 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / Gene: crt, MXAN_3757 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1D5Y4, 3-hydroxybutyryl-CoA dehydratase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1126 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 60% Tacsimate pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.7994 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7994 Å / Relative weight: 1
ReflectionResolution: 1.1→42.88 Å / Num. obs: 326543 / % possible obs: 99.1 % / Redundancy: 13.3 % / Biso Wilson estimate: 11.41 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.073 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.1-1.1212.91.288197.9
6.02-42.8812.70.03199.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JBW

5jbw


Resolution: 1.1→42.387 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.47
RfactorNum. reflection% reflection
Rfree0.1446 16101 4.93 %
Rwork0.1249 --
obs0.1259 326352 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.2 Å2 / Biso mean: 16.8208 Å2 / Biso min: 6.71 Å2
Refinement stepCycle: final / Resolution: 1.1→42.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5781 0 205 1174 7160
Biso mean--23.42 30.41 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076322
X-RAY DIFFRACTIONf_angle_d1.0978631
X-RAY DIFFRACTIONf_chiral_restr0.075999
X-RAY DIFFRACTIONf_plane_restr0.0071145
X-RAY DIFFRACTIONf_dihedral_angle_d22.8742486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.11250.22275250.2109101391066498
1.1125-1.12560.19155520.1942100711062398
1.1256-1.13930.20665300.1835101271065798
1.1393-1.15370.19454980.1702102291072798
1.1537-1.16890.18375310.1617101471067898
1.1689-1.18490.16795230.1553101251064898
1.1849-1.20190.17935180.151102391075798
1.2019-1.21980.17515160.1544102161073298
1.2198-1.23890.16625310.1496102231075498
1.2389-1.25920.15895520.1362101971074999
1.2592-1.28090.15685240.1315102401076499
1.2809-1.30420.15465130.1315103131082699
1.3042-1.32930.1655410.1257102381077999
1.3293-1.35640.13945160.1161102641078099
1.3564-1.38590.14295370.1136103191085699
1.3859-1.41810.14655320.1112103331086599
1.4181-1.45360.13455390.1105103201085999
1.4536-1.49290.12755370.1049103321086999
1.4929-1.53680.12065190.101103851090499
1.5368-1.58650.12635750.10021037210947100
1.5865-1.64320.12595630.10281035810921100
1.6432-1.7090.13085140.10541042710941100
1.709-1.78670.13335330.11081044710980100
1.7867-1.88090.12345340.11311048711021100
1.8809-1.99880.13035280.12211044810976100
1.9988-2.15310.13035580.11511050311061100
2.1531-2.36980.12855340.1171052711061100
2.3698-2.71260.1485760.12411056811144100
2.7126-3.41740.155660.13161067111237100
3.4174-42.4180.15245860.13151098611572100

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