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- PDB-7cw1: Crystal structure of a biodegradable plastic-degrading cutinase-l... -

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Basic information

Entry
Database: PDB / ID: 7cw1
TitleCrystal structure of a biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast, Pseudozyma antarctica, solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).
ComponentsCutinase-like enzyme
KeywordsHYDROLASE / cutinase-like enzyme / biodegradable plastic degrading enzyme / alpha/beta hydrolase fold
Function / homologyCutinase / Cutinase/acetylxylan esterase / Cutinase / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / CACODYLIC ACID / Cutinase-like enzyme
Function and homology information
Biological speciesPseudozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSuzuki, K.
CitationJournal: To Be Published
Title: Crystal structure of a biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast, Pseudozyma antarctica, solved by getting the phase from anomalous scattering of ...Title: Crystal structure of a biodegradable plastic-degrading cutinase-like enzyme from the phyllosphere yeast, Pseudozyma antarctica, solved by getting the phase from anomalous scattering of uncovalently coordinated arsenic (cacodylate).
Authors: Suzuki, K.
History
DepositionAug 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cutinase-like enzyme
B: Cutinase-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0525
Polymers40,7532
Non-polymers2993
Water6,503361
1
A: Cutinase-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5383
Polymers20,3771
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area8400 Å2
MethodPISA
2
B: Cutinase-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5152
Polymers20,3771
Non-polymers1381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.065, 61.587, 110.387
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cutinase-like enzyme


Mass: 20376.658 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudozyma antarctica (fungus) / References: UniProt: S6BC01
#2: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE


Mass: 137.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7AsO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 1.839 Å3/Da / Density % sol: 33.157 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.17M Sodium acetate trihydrate, 0.085M Sodium cacodylate trihydrate , 25.5%w/v Polyethylene glycol 8000, 15%w/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 25, 2017
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→55.19 Å / Num. obs: 33315 / % possible obs: 98.3 % / Redundancy: 12.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.034 / Rrim(I) all: 0.122 / Net I/σ(I): 17 / Num. measured all: 428388 / Scaling rejects: 602
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
1.7-1.7312.90.4872175316880.9330.1390.507596
8.99-55.1911.30.028321728510.0080.033599.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
xia20.6.2data reduction
CRANK22.0.229phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→55.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.913 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 1713 5.2 %RANDOM
Rwork0.1558 ---
obs0.1576 31548 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.97 Å2 / Biso mean: 9.31 Å2 / Biso min: 3.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2---0.27 Å20 Å2
3---0.41 Å2
Refinement stepCycle: final / Resolution: 1.7→55.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 11 361 3218
Biso mean--21.61 17.5 -
Num. residues----394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132910
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172586
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.6453962
X-RAY DIFFRACTIONr_angle_other_deg1.5941.5746014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6735392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16223.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06115422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6031512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023376
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
LS refinement shellResolution: 1.7→1.743 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.245 119 -
Rwork0.174 2239 -
obs--96.17 %

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