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- PDB-7xwv: Feruloyl-CoA hydratase/lyase complexed with Vanillin and Coenzyme A -

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Basic information

Entry
Database: PDB / ID: 7xwv
TitleFeruloyl-CoA hydratase/lyase complexed with Vanillin and Coenzyme A
ComponentsFeruloyl-CoA hydratase/lyase
KeywordsLYASE / Feruloyl-CoA hydratase/lyase
Function / homology: / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / lyase activity / COENZYME A / IMIDAZOLE / 4-hydroxy-3-methoxybenzaldehyde / Feruloyl-CoA hydratase/lyase
Function and homology information
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsSeok, J. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Production of various phenolic aldehyde compounds using the 4CL-FCHL biosynthesis platform.
Authors: Seok, J. / Seo, H. / Hong, J. / Kim, K.J.
History
DepositionMay 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Feruloyl-CoA hydratase/lyase
B: Feruloyl-CoA hydratase/lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,50311
Polymers67,2262
Non-polymers2,2779
Water2,828157
1
A: Feruloyl-CoA hydratase/lyase
B: Feruloyl-CoA hydratase/lyase
hetero molecules

A: Feruloyl-CoA hydratase/lyase
B: Feruloyl-CoA hydratase/lyase
hetero molecules

A: Feruloyl-CoA hydratase/lyase
B: Feruloyl-CoA hydratase/lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,50933
Polymers201,6796
Non-polymers6,83027
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area37630 Å2
ΔGint-120 kcal/mol
Surface area45940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.471, 132.471, 241.533
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Feruloyl-CoA hydratase/lyase


Mass: 33613.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Gene: ferB / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8RR28

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Non-polymers , 5 types, 166 molecules

#2: Chemical ChemComp-V55 / 4-hydroxy-3-methoxybenzaldehyde / p-vanillin


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.03 Å3/Da / Density % sol: 59.45 % / Mosaicity: 0.812 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium phosphate dibasic, Imidazole/Hydrochloric acid

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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 30, 2018
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: 1.81→50 Å / Num. obs: 71335 / % possible obs: 96.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.033 / Rrim(I) all: 0.101 / Χ2: 4.684 / Net I/σ(I): 16.7 / Num. measured all: 458140
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.81-1.842.90.32432400.4440.1980.3831.49689.4
1.84-1.873.20.30933540.5040.1790.361.56191.6
1.87-1.913.40.29333650.6270.1660.3391.62492
1.91-1.953.60.27534040.7320.1490.3151.70493.7
1.95-1.9940.2534550.8340.1260.2821.98495
1.99-2.044.60.22935160.8850.1080.2552.2396.5
2.04-2.094.90.21735820.9070.0990.242.47597.1
2.09-2.155.10.19735250.9390.0870.2162.79597.3
2.15-2.215.40.18235650.9540.0780.1993.12397.1
2.21-2.285.80.16935600.9660.070.1833.54397.3
2.28-2.366.10.15936240.9710.0640.1723.77898.1
2.36-2.466.30.15235940.9770.060.1644.07998.5
2.46-2.576.70.14136420.980.0540.1524.33798.6
2.57-2.77.20.1336150.9850.0480.1394.55698.6
2.7-2.877.80.12136460.9870.0430.1285.27499.1
2.87-3.098.70.10836640.9910.0370.1145.99799.4
3.09-3.419.60.09736830.9940.0320.1026.54799.5
3.41-3.910.20.08437120.9950.0270.0896.95999.9
3.9-4.9110.60.07437520.9970.0230.0776.94899.9
4.91-5010.30.06838370.9960.0220.0715.31899

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j5i

2j5i


Resolution: 1.81→30.65 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.888 / SU B: 3.071 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3561 5 %RANDOM
Rwork0.2201 ---
obs0.2218 67774 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.18 Å2 / Biso mean: 22.511 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.81→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3928 0 153 157 4238
Biso mean--47.13 27.83 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153863
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.6525652
X-RAY DIFFRACTIONr_angle_other_deg1.3751.5848840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0315486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2121.639244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18615680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5731534
X-RAY DIFFRACTIONr_chiral_restr0.0840.2498
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021035
LS refinement shellResolution: 1.815→1.862 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 237 -
Rwork0.346 4537 -
all-4774 -
obs--88.51 %

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