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- PDB-6l3p: Crystal strcuture of Feruloyl-CoA hydratase lyase(FCHL) complexed... -

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Basic information

Entry
Database: PDB / ID: 6l3p
TitleCrystal strcuture of Feruloyl-CoA hydratase lyase(FCHL) complexed with CoA
ComponentsHydroxycinnamoyl-CoA hydratase-lyase
KeywordsLYASE / Feruloyl-CoA hydratae lyase
Function / homology
Function and homology information


vanillin synthase / trans-feruloyl-CoA hydratase / :
Similarity search - Function
Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily
Similarity search - Domain/homology
COENZYME A / Hydroxycinnamoyl-CoA hydratase-lyase
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeok, J. / Seo, H. / Kim, K.-J.
CitationJournal: to be published
Title: Kinetic and structural analysis for bioproduction of vanillin by feruloyl-CoA hydratase/lyase from Pseudomonas putida KT2440
Authors: Seok, J. / Seo, H. / Kim, K.-J.
History
DepositionOct 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Hydroxycinnamoyl-CoA hydratase-lyase
B: Hydroxycinnamoyl-CoA hydratase-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2439
Polymers64,2472
Non-polymers1,9967
Water46826
1
A: Hydroxycinnamoyl-CoA hydratase-lyase
B: Hydroxycinnamoyl-CoA hydratase-lyase
hetero molecules

A: Hydroxycinnamoyl-CoA hydratase-lyase
B: Hydroxycinnamoyl-CoA hydratase-lyase
hetero molecules

A: Hydroxycinnamoyl-CoA hydratase-lyase
B: Hydroxycinnamoyl-CoA hydratase-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,72827
Polymers192,7426
Non-polymers5,98721
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area33120 Å2
ΔGint-150 kcal/mol
Surface area52630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.781, 136.781, 242.723
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Hydroxycinnamoyl-CoA hydratase-lyase


Mass: 32123.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: PP_3358 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q88HJ8, vanillin synthase, trans-feruloyl-CoA hydratase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.4 Å3/Da / Density % sol: 63.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 25% propanediol, PEG3000, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2019
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 29931 / % possible obs: 98.5 % / Redundancy: 11.2 % / CC1/2: 0.995 / Rpim(I) all: 0.022 / Rrim(I) all: 0.084 / Net I/σ(I): 38.3
Reflection shellResolution: 2.5→2.56 Å / Num. unique obs: 2038 / CC1/2: 0.935

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j5i

2j5i


Resolution: 2.5→31.52 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.884 / SU B: 11.473 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.273
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1451 4.8 %RANDOM
Rwork0.2358 ---
obs0.2382 28480 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 129.06 Å2 / Biso mean: 47.723 Å2 / Biso min: 11.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2.5→31.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 126 26 4007
Biso mean--62.51 36.26 -
Num. residues----487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0144052
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173660
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.6975489
X-RAY DIFFRACTIONr_angle_other_deg0.9161.6658569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3185483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38821.925213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.47815700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0021532
X-RAY DIFFRACTIONr_chiral_restr0.070.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024463
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02735
LS refinement shellResolution: 2.502→2.567 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 102 -
Rwork0.396 2038 -
all-2140 -
obs--97.01 %

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