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- PDB-7cqb: Crystal structure of mutant of a Petase mutant -

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Basic information

Entry
Database: PDB / ID: 7cqb
TitleCrystal structure of mutant of a Petase mutant
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / Poly(ethylene terephthalate) hydrolase / substrate binding / inhibitor
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function
Dienelactone hydrolase / Dienelactone hydrolase family / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsHan, X. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)3180062 China
Chinese Academy of SciencesKFJ-STS-ZDTP-064 China
CitationJournal: to be published
Title: Crystal structure of mutant of a Petase mutant
Authors: Han, X. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
History
DepositionAug 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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


Theoretical massNumber of molelcules
Total (without water)28,9921
Polymers28,9921
Non-polymers00
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9670 Å2
Unit cell
Length a, b, c (Å)51.065, 51.264, 84.806
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 / PETase / PET-digesting enzyme


Mass: 28992.152 Da / Num. of mol.: 1 / Mutation: N233A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6) (bacteria)
Strain: NBRC 110686 / TISTR 2288 / 201-F6 / Gene: ISF6_4831 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: POLYETHYLENE GLYCOL 6000, GLYCEROL, MES, PH 6.0,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→25 Å / Num. obs: 19219 / % possible obs: 99.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.038 / Rrim(I) all: 0.094 / Χ2: 1.235 / Net I/σ(I): 8 / Num. measured all: 121346
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.86-1.936.40.38318920.9330.1640.4170.64299.9
1.93-26.70.2918950.9570.1230.3160.73100
2-2.096.70.23118940.9730.0980.2520.84899.9
2.09-2.216.60.17819020.9790.0770.1940.98599.4
2.21-2.346.50.14519100.9820.0640.1591.03399.7
2.34-2.526.40.11818900.9890.0520.1291.11999.2
2.52-2.786.20.09418990.9910.0420.1031.26398.1
2.78-3.185.90.0719180.9940.0330.0781.44498
3.18-45.60.05919410.9950.0280.0662.17399
4-2560.05420780.9960.0240.0592.28299.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XG0

5xg0


Resolution: 1.86→24.77 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.809 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1916 896 4.7 %RANDOM
Rwork0.1424 ---
obs0.1447 18274 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.39 Å2 / Biso mean: 20.054 Å2 / Biso min: 6.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0 Å20 Å2
2---1.1 Å20 Å2
3---2.27 Å2
Refinement stepCycle: final / Resolution: 1.86→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 0 233 2149
Biso mean---32.48 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131967
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171731
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.6422683
X-RAY DIFFRACTIONr_angle_other_deg1.5051.5664029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87221.46189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47715286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3071513
X-RAY DIFFRACTIONr_chiral_restr0.080.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
LS refinement shellResolution: 1.86→1.908 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 90 -
Rwork0.198 1305 -
all-1395 -
obs--99.36 %

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