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- PDB-7yme: Crystal structure of a PET hydrolase M9 variant from Cryptosporan... -

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Basic information

Entry
Database: PDB / ID: 7yme
TitleCrystal structure of a PET hydrolase M9 variant from Cryptosporangium aurantiacum
ComponentsPoly(Ethylene terephthalate) hydrolase
KeywordsHYDROLASE / Poly(Ethylene terephthalate) hydrolase / esterase
Function / homologyAlpha/Beta hydrolase fold / Cutinase
Function and homology information
Biological speciesCryptosporangium aurantiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKi, D. / Hong, H. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Discovery and rational engineering of PET hydrolase with both mesophilic and thermophilic PET hydrolase properties.
Authors: Hong, H. / Ki, D. / Seo, H. / Park, J. / Jang, J. / Kim, K.J.
History
DepositionJul 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(Ethylene terephthalate) hydrolase
B: Poly(Ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)66,0972
Polymers66,0972
Non-polymers00
Water8,161453
1
A: Poly(Ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)33,0481
Polymers33,0481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(Ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)33,0481
Polymers33,0481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.019, 112.307, 112.538
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 Poly(Ethylene terephthalate) hydrolase


Mass: 33048.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 9M variant
Source: (gene. exp.) Cryptosporangium aurantiacum (bacteria)
Gene: SAMN05443668_101498 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1M7II12
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 1.96 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG monomethyl ether 5000, 0.1 M HEPES pH7.0, 5% (v/v) Tascimate pH 7.0

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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: Jun 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 84276 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.034 / Rrim(I) all: 0.09 / Χ2: 1.4 / Net I/σ(I): 7.4 / Num. measured all: 606538
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.537.20.82941490.7790.330.8930.949100
1.53-1.557.20.70941540.8190.2820.7640.992100
1.55-1.587.20.59341970.8650.2360.6381.019100
1.58-1.627.30.54141060.8940.2150.5821.04100
1.62-1.657.30.48241720.9090.1920.5191.068100
1.65-1.697.30.4141600.9330.1630.4411.102100
1.69-1.737.30.32741910.9510.130.3521.145100
1.73-1.787.30.27141780.9670.1080.2911.205100
1.78-1.837.30.2341610.9750.0920.2481.269100
1.83-1.897.30.18541860.9830.0740.1991.327100
1.89-1.967.30.15442010.9880.0610.1661.437100
1.96-2.047.30.13141850.990.0520.1421.502100
2.04-2.137.30.11141930.9920.0440.121.562100
2.13-2.247.30.09742110.9940.0390.1051.638100
2.24-2.387.20.08742220.9950.0350.0941.654100
2.38-2.567.20.07542610.9960.030.0811.613100
2.56-2.827.20.06642160.9970.0270.0721.657100
2.82-3.237.20.0642980.9970.0240.0651.732100
3.23-4.077.10.05443280.9970.0220.0582.001100
4.07-506.50.05345070.9960.0230.0582.10199.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YM9

7ym9


Resolution: 1.5→39.78 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.369 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 4290 5.1 %RANDOM
Rwork0.1763 ---
obs0.1776 79902 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.21 Å2 / Biso mean: 17.159 Å2 / Biso min: 8.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å20 Å2
2--0.29 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.5→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3935 0 0 453 4388
Biso mean---28.66 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134068
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143679
X-RAY DIFFRACTIONr_angle_refined_deg1.751.6495574
X-RAY DIFFRACTIONr_angle_other_deg1.5661.5728465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0385518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.94421.066197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07715563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5241528
X-RAY DIFFRACTIONr_chiral_restr0.0960.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02994
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 300 -
Rwork0.268 5790 -
all-6090 -
obs--99.48 %

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