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- PDB-2j5i: Crystal Structure of Hydroxycinnamoyl-CoA Hydratase-Lyase -

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Basic information

Entry
Database: PDB / ID: 2j5i
TitleCrystal Structure of Hydroxycinnamoyl-CoA Hydratase-Lyase
Components(P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE) x 3
KeywordsLYASE / VANILLIN / ALDOLASE / CROTONASE / HYDRATASE / COENZYME-A
Function / homology
Function and homology information


feruloyl-CoA hydratase/lyase / feruloyl-CoA hydratase/lyase activity / : / isoprenoid catabolic process
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2850 / : / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2850 / : / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / ClpP/crotonase-like domain superfamily / Helix non-globular / Special / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Hydroxycinnamoyl-CoA hydratase-lyase
Similarity search - Component
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLeonard, P.M. / Brzozowski, A.M. / Lebedev, A. / Marshall, C.M. / Smith, D.J. / Verma, C.S. / Walton, N.J. / Grogan, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: The 1.8 A Resolution Structure of Hydroxycinnamoyl- Coenzyme a Hydratase-Lyase (Hchl) from Pseudomonas Fluorescens, an Enzyme that Catalyses the Transformation of Feruloyl-Coenzyme a to Vanillin.
Authors: Leonard, P.M. / Brzozowski, A.M. / Lebedev, A. / Marshall, C.M. / Smith, D.J. / Verma, C.S. / Walton, N.J. / Grogan, G.
History
DepositionSep 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
B: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
C: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
D: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
E: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
F: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
G: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
H: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
I: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
J: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
K: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
L: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE


Theoretical massNumber of molelcules
Total (without water)372,50212
Polymers372,50212
Non-polymers00
Water33,5261861
1
A: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
B: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
C: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
D: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
E: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
F: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE


Theoretical massNumber of molelcules
Total (without water)186,2366
Polymers186,2366
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
H: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
I: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
J: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
K: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE
L: P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE


Theoretical massNumber of molelcules
Total (without water)186,2676
Polymers186,2676
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)154.238, 167.487, 130.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 249
2114B2 - 249
3114C2 - 249
4114D2 - 249
5114E2 - 249
6114F2 - 249
7114G2 - 249
8114H2 - 249
9114I2 - 249
10114J2 - 249
11114K2 - 249
12114L2 - 249

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Components

#1: Protein P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE / HYDROXYCINNAMOYL-COENZYME-A HYDRATASE-LYASE


Mass: 31012.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSITUTES OF FOOD RESEARCH, NORWICH U.K. / Plasmid: PFI3009 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase
#2: Protein
P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE / HYDROXYCINNAMOYL-COENZYME-A HYDRATASE-LYASE


Mass: 31044.613 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSITUTES OF FOOD RESEARCH, NORWICH U.K. / Plasmid: PFI3009 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase
#3: Protein P-HYDROXYCINNAMOYL COA HYDRATASE/LYASE / HYDROXYCINNAMOYL-COENZYME-A HYDRATASE-LYASE


Mass: 31043.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: AN103 / Description: INSITUTES OF FOOD RESEARCH, NORWICH U.K. / Plasmid: PFI3009 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O69762, trans-feruloyl-CoA hydratase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1861 / 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: 2.42 Å3/Da / Density % sol: 49.5 %
Crystal growpH: 5.6
Details: PEG 20000 11% W/V PEG 550 MME 8% V/V 0.8M NA FORMATE BUTANE-1,4-DIOL 0,2% V/V 0.05M MES PH 5.6

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 308927 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.9
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UIY

1uiy


Resolution: 1.8→111.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 15557 5.1 %RANDOM
Rwork0.179 ---
obs0.181 292487 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--2.38 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→111.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23260 0 0 1861 25121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02223227
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.96431502
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8652980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49523.994984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55153987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.87815168
X-RAY DIFFRACTIONr_chiral_restr0.1410.23510
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217521
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.212012
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.216201
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.21836
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.279
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9671.514673
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.634223433
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.92438554
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5984.58050
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1716 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.240.5
2Bmedium positional0.240.5
3Cmedium positional0.220.5
4Dmedium positional0.260.5
5Emedium positional0.250.5
6Fmedium positional0.240.5
7Gmedium positional0.230.5
8Hmedium positional0.190.5
9Imedium positional0.190.5
10Jmedium positional0.190.5
11Kmedium positional0.190.5
12Lmedium positional0.230.5
1Amedium thermal1.852
2Bmedium thermal2.12
3Cmedium thermal1.792
4Dmedium thermal1.662
5Emedium thermal1.372
6Fmedium thermal1.912
7Gmedium thermal2.692
8Hmedium thermal1.52
9Imedium thermal1.82
10Jmedium thermal1.32
11Kmedium thermal1.272
12Lmedium thermal1.572
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 1165
Rwork0.229 20775

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