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- PDB-29cu: Crystal Structure of a Cutinase from Saccharopolyspora Dendranthemae -

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Basic information

Entry
Database: PDB / ID: 29cu
TitleCrystal Structure of a Cutinase from Saccharopolyspora Dendranthemae
ComponentsCutinase
KeywordsHYDROLASE / poly(ethylene terephthalate) hydrolase / cutinase
Function / homologyCutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Cutinase
Function and homology information
Biological speciesSaccharopolyspora dendranthemae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsWain, B. / Pickford, A.R. / Wood, S.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Y007972/1 United Kingdom
CitationJournal: To Be Published
Title: Examining PETase Activity Across a Phylogenetic Genus: Investigating Thermostability and the Effect of a Single Surface-Charge-Altering Substitution on PET Film Degradation
Authors: Wain, B. / Pickford, A.R. / Tornesakis, K. / Cox, P. / Rudge, E. / Figueiredo, F. / Wood, S.
History
DepositionMar 6, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6582
Polymers28,5661
Non-polymers921
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.502, 61.707, 88.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cutinase


Mass: 28565.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora dendranthemae (bacteria)
Gene: FHU35_111186
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A561VAE2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.83 Å3/Da / Density % sol: 32.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: Crystals were grown by sitting drop vapor diffusion at 4 degrees C. Drops were set up by mixing 1 uL of protein solution (10 mg/mL in Y sodium phosphate buffer, pH 7.5) with 1 uL of ...Details: Crystals were grown by sitting drop vapor diffusion at 4 degrees C. Drops were set up by mixing 1 uL of protein solution (10 mg/mL in Y sodium phosphate buffer, pH 7.5) with 1 uL of reservoir solution (0.2 M Sodium Fluoride, 20% (w/v) PEG 3350, unbuffered). The drops were incubated for 9 months. The setup was performed using a TTP Labtech Mosquito liquid handling robot.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.13→50.55 Å / Num. obs: 67263 / % possible obs: 84.1 % / Redundancy: 11.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.06 / Net I/σ(I): 21.8
Reflection shellResolution: 1.13→1.2 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 443 / CC1/2: 0.65 / Rrim(I) all: 0.65 / % possible all: 11.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROCdata scaling
autoPROCdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→50.55 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.958 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14444 3358 5 %RANDOM
Rwork0.11981 ---
obs0.12105 63583 83.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.843 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å2-0 Å20 Å2
2---1.27 Å2-0 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.13→50.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 6 277 2196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122096
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161879
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.8142886
X-RAY DIFFRACTIONr_angle_other_deg0.6391.7364389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.958510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.22110302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022514
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02432
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0430.7951081
X-RAY DIFFRACTIONr_mcbond_other3.020.7951081
X-RAY DIFFRACTIONr_mcangle_it4.3841.4321369
X-RAY DIFFRACTIONr_mcangle_other4.3891.4361370
X-RAY DIFFRACTIONr_scbond_it4.8870.9921015
X-RAY DIFFRACTIONr_scbond_other4.8850.9921016
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7421.7451518
X-RAY DIFFRACTIONr_long_range_B_refined12.90211.362377
X-RAY DIFFRACTIONr_long_range_B_other11.2989.772301
X-RAY DIFFRACTIONr_rigid_bond_restr4.28833975
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.13→1.157 Å
RfactorNum. reflection% reflection
Rfree0.291 33 -
Rwork0.23 714 -
obs--12.74 %

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