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- PDB-7cy9: Crystal structure of a biodegradable plastic-degrading cutinase f... -

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Entry
Database: PDB / ID: 7cy9
TitleCrystal structure of a biodegradable plastic-degrading cutinase from Paraphoma sp. B47-9 solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).
ComponentsCutinase
KeywordsHYDROLASE / Serine hydrolase / Cutinase / Biodegradable plastic-degrading enzyme / cacodylate
Function / homology
Function and homology information


cutinase activity / cutinase / extracellular region
Similarity search - Function
Cutinase, monofunctional / Cutinase, aspartate and histidine active sites / Cutinase, serine active site / Cutinase, serine active site. / Cutinase, aspartate and histidine active sites. / Cutinase / Cutinase/acetylxylan esterase / Cutinase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
CACODYLIC ACID / Cutinase
Similarity search - Component
Biological speciesParaphoma sp. B47-9 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.36 Å
AuthorsSuzuki, K. / Koitabashi, M.
CitationJournal: To Be Published
Title: Crystal structure of a biodegradable plastic-degrading cutinase from Paraphoma sp. B47-9 solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).
Authors: Suzuki, K. / Koitabashi, M.
History
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 2.0Dec 16, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / citation_author / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_rmsd_bond.bond_deviation / _pdbx_validate_rmsd_bond.bond_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.classification / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Model orientation/position / Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cutinase
B: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4119
Polymers39,9052
Non-polymers5067
Water6,485360
1
A: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2745
Polymers19,9521
Non-polymers3224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area8200 Å2
MethodPISA
2
B: Cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1364
Polymers19,9521
Non-polymers1843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area7920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.886, 43.517, 51.724
Angle α, β, γ (deg.)103.780, 92.420, 101.490
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cutinase /


Mass: 19952.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paraphoma sp. B47-9 (fungus) / References: UniProt: A0A060N399, cutinase
#2: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE / Cacodylic acid


Mass: 137.997 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H7AsO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
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: 1.865 Å3/Da / Density % sol: 34.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium acetate, 0.1M Sodium cacodylate, 1mM Calcium chloride, 30% w/v Polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→36.69 Å / Num. obs: 55832 / % possible obs: 89.9 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.037 / Rrim(I) all: 0.074 / Net I/σ(I): 16.2 / Num. measured all: 218677 / Scaling rejects: 93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.36-1.383.80.3341080228470.8930.1980.3894.186.7
7.19-36.693.70.03214293860.9960.0210.03939.592.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
SHELXphasing
PDB_EXTRACT3.25data extraction
xia20.6.0data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.36→36.69 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.024 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1659 2857 5.1 %RANDOM
Rwork0.122 ---
obs0.1242 52937 89.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.81 Å2 / Biso mean: 9.15 Å2 / Biso min: 4.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20.6 Å21 Å2
2--0.1 Å20.38 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 1.36→36.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 19 360 3158
Biso mean--13.83 19.27 -
Num. residues----387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132838
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172707
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.643860
X-RAY DIFFRACTIONr_angle_other_deg1.6731.5856204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5821.97132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49815424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0631520
X-RAY DIFFRACTIONr_chiral_restr0.1140.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02644
X-RAY DIFFRACTIONr_rigid_bond_restr7.27135545
LS refinement shellResolution: 1.36→1.395 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.227 210 -
Rwork0.158 3898 -
obs--89.52 %

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