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- PDB-6l3o: Crystal strcuture of Feruloyl-CoA hydratase lyase(FCHL) from Pseu... -

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Basic information

Entry
Database: PDB / ID: 6l3o
TitleCrystal strcuture of Feruloyl-CoA hydratase lyase(FCHL) from Pseudomonas putida KT2440
ComponentsHydroxycinnamoyl-CoA hydratase-lyase
KeywordsLYASE / Feruloyl-CoA hydratae lyase
Function / homology
Function and homology information


vanillin synthase / trans-feruloyl-CoA hydratase / isoprenoid catabolic process / lyase activity
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
Hydroxycinnamoyl-CoA hydratase-lyase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 12, 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


Theoretical massNumber of molelcules
Total (without water)64,2472
Polymers64,2472
Non-polymers00
Water2,504139
1
A: Hydroxycinnamoyl-CoA hydratase-lyase
B: Hydroxycinnamoyl-CoA hydratase-lyase

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

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


Theoretical massNumber of molelcules
Total (without water)192,7426
Polymers192,7426
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area28950 Å2
ΔGint-129 kcal/mol
Surface area47440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.745, 87.745, 198.223
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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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 (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 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: Apr 5, 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: 1.65→50 Å / Num. obs: 68160 / % possible obs: 99.7 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.027 / Rrim(I) all: 0.058 / Χ2: 1.66 / Net I/σ(I): 12.1 / Num. measured all: 297935
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.683.80.28733970.9460.1610.331.15598.4
1.68-1.714.20.24633770.9640.1320.2811.23499.9
1.71-1.744.20.22733950.9710.1210.2591.34499.8
1.74-1.784.20.18534300.9820.0980.211.40899.9
1.78-1.824.20.17333970.9820.0910.1961.50499.9
1.82-1.864.20.14734450.9810.0770.1661.70699.9
1.86-1.94.30.13534230.9880.0710.1531.74399.8
1.9-1.964.30.11434080.9860.0590.1291.87999.9
1.96-2.014.30.10333790.9810.0530.1162.01299.9
2.01-2.084.40.08934380.9940.0460.11.834100
2.08-2.154.40.07733930.9960.0390.0861.79499.8
2.15-2.244.40.07134380.9970.0360.081.69799.9
2.24-2.344.50.06533840.9960.0330.0731.67999.8
2.34-2.464.50.05834090.9970.0290.0651.61299.8
2.46-2.624.50.05434360.9970.0270.0611.60899.9
2.62-2.824.60.0534040.9980.0250.0561.57299.9
2.82-3.114.60.04834250.9970.0240.0541.61999.9
3.11-3.554.60.04234100.9980.0210.0471.59899.9
3.55-4.484.60.0434130.9970.0210.0451.79299.9
4.48-504.40.04433590.9950.0240.052.27998

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J5I

2j5i


Resolution: 1.65→30.17 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.826 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 3382 5 %RANDOM
Rwork0.1748 ---
obs0.1763 64777 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.71 Å2 / Biso mean: 29.7 Å2 / Biso min: 14.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.65→30.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 0 139 4058
Biso mean---32.17 -
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134007
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173756
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.6415430
X-RAY DIFFRACTIONr_angle_other_deg1.5151.5778690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.63322.037216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.18915705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4821532
X-RAY DIFFRACTIONr_chiral_restr0.0940.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
LS refinement shellResolution: 1.651→1.694 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 273 -
Rwork0.263 4714 -
all-4987 -
obs--98.5 %

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