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- PDB-7xwc: Feruloyl-CoA hydratase/lyase from Sphingomonas paucimobilis SYK-6 -

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Basic information

Entry
Database: PDB / ID: 7xwc
TitleFeruloyl-CoA hydratase/lyase from Sphingomonas paucimobilis SYK-6
ComponentsFeruloyl-CoA hydratase/lyase
KeywordsLYASE / Feruloyl-CoA hydratase/lyase
Function / homologyisoprenoid catabolic process / : / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / lyase activity / DI(HYDROXYETHYL)ETHER / Feruloyl-CoA hydratase/lyase
Function and homology information
Biological speciesSphingomonas paucimobilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.986 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 26, 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)67,7297
Polymers67,2262
Non-polymers5035
Water3,351186
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)203,18621
Polymers201,6796
Non-polymers1,50815
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 area32210 Å2
ΔGint-105 kcal/mol
Surface area47270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.839, 132.839, 239.621
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 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
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 59.35 % / 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: Feb 14, 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: 1.98→50 Å / Num. obs: 55694 / % possible obs: 99 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.029 / Rrim(I) all: 0.095 / Χ2: 3.149 / Net I/σ(I): 13.9 / Num. measured all: 481144
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.015.10.326810.770.1350.3311.35596.8
2.01-2.055.70.28727600.8250.1230.3141.51798.4
2.05-2.095.80.27427230.8740.1150.2981.56298.8
2.09-2.136.10.25627640.8980.1030.2771.81598.7
2.13-2.186.50.23527470.9340.0920.2541.94298.8
2.18-2.236.70.22727430.9410.0870.2452.02598.8
2.23-2.297.10.20127630.960.0740.2152.29198.9
2.29-2.357.30.19227620.9680.070.2052.26799
2.35-2.427.60.18327820.4890.0660.1952.53498.9
2.42-2.497.80.17527930.9780.0610.1862.52399.3
2.49-2.588.40.15627540.9850.0530.1652.71199
2.58-2.698.80.14827680.9870.0490.1562.88999
2.69-2.819.20.13327800.9910.0430.143.22699
2.81-2.969.90.11927800.9940.0370.1243.50499.2
2.96-3.1410.50.10728200.9950.0320.1123.77299.4
3.14-3.3911.10.09627890.9960.0280.14.12799.4
3.39-3.73120.08228330.9970.0240.0864.33699.9
3.73-4.2612.40.06928400.9980.020.0724.54999.8
4.26-5.3712.50.0628550.9990.0170.0624.04799.8
5.37-5011.70.05929570.9990.0180.0623.69699.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J5I

2j5i


Resolution: 1.986→35.21 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.408 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 2762 5 %RANDOM
Rwork0.184 ---
obs0.1856 52932 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.87 Å2 / Biso mean: 27.074 Å2 / Biso min: 12.72 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.986→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3935 0 33 186 4154
Biso mean--42.68 30.95 -
Num. residues----489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134055
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153804
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6455479
X-RAY DIFFRACTIONr_angle_other_deg1.4161.5838707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1495487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73421.833240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82915681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3411534
X-RAY DIFFRACTIONr_chiral_restr0.0810.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021011
LS refinement shellResolution: 1.986→2.037 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 202 -
Rwork0.298 3802 -
all-4004 -
obs--97.18 %

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