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- PDB-7dzu: Cyrstal structure of PETase K169A mutant from Rhizobacter gummiphilus -

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Basic information

Entry
Database: PDB / ID: 7dzu
TitleCyrstal structure of PETase K169A mutant from Rhizobacter gummiphilus
ComponentsDLH domain-containing protein
KeywordsHYDROLASE / PET hydrolase
Function / homologyCutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / PET hydrolase/cutinase-like domain-containing protein
Function and homology information
Biological speciesRhizobacter gummiphilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSagong, H.-Y. / Kim, K.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020M3A9I5037635 Korea, Republic Of
CitationJournal: J Hazard Mater / Year: 2021
Title: Implications for the PET decomposition mechanism through similarity and dissimilarity between PETases from Rhizobacter gummiphilus and Ideonella sakaiensis.
Authors: Sagong, H.Y. / Son, H.F. / Seo, H. / Hong, H. / Lee, D. / Kim, K.J.
History
DepositionJan 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DLH domain-containing protein


Theoretical massNumber of molelcules
Total (without water)28,4791
Polymers28,4791
Non-polymers00
Water1,874104
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 area10380 Å2
Unit cell
Length a, b, c (Å)51.139, 54.106, 110.136
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 DLH domain-containing protein


Mass: 28478.609 Da / Num. of mol.: 1 / Mutation: K169A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobacter gummiphilus (bacteria) / Strain: NS21 / Gene: A4W93_05950 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami-B / References: UniProt: A0A1W6L588
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.02 % / Mosaicity: 1.331 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5 / Details: NaCl, HEPES

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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: Dec 17, 2020
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12259 / % possible obs: 98.1 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.051 / Rrim(I) all: 0.124 / Χ2: 3.428 / Net I/σ(I): 11.6 / Num. measured all: 71359
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.446.30.4145930.9330.1760.4512.56298.3
2.44-2.496.30.3936000.9410.1660.4282.38597.4
2.49-2.536.30.3615930.9520.1540.3932.45197.2
2.53-2.596.20.3496040.960.1490.3812.59397.6
2.59-2.646.30.2875710.9690.1220.3132.68396.9
2.64-2.76.10.266230.9740.1130.2842.69997.8
2.7-2.776.20.2235800.9820.0960.2432.84296.7
2.77-2.8560.2226060.980.0970.2433.17797.1
2.85-2.936.10.1735810.9830.0760.193.22898
2.93-3.025.90.176290.980.0740.1863.56197.8
3.02-3.135.80.1395890.9870.0610.1523.78298.2
3.13-3.265.80.1286150.990.0570.143.898.6
3.26-3.415.60.1166150.990.0530.1284.05197.6
3.41-3.585.50.0966010.9920.0440.1064.13698.4
3.58-3.815.40.0896160.9930.0420.0994.38798.7
3.81-4.15.30.086280.9940.0370.0884.38698.9
4.1-4.525.40.0756220.9930.0350.0834.4798.9
4.52-5.175.50.0696470.9960.0310.0764.16299.7
5.17-6.515.70.076530.9960.0310.0773.721100
6.51-505.10.0646930.9950.0310.0724.1897.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DZT

7dzt


Resolution: 2.4→27.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.033 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 634 5.2 %RANDOM
Rwork0.183 ---
obs0.1865 11585 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.07 Å2 / Biso mean: 31.98 Å2 / Biso min: 6.55 Å2
Baniso -1Baniso -2Baniso -3
1--3.24 Å20 Å20 Å2
2--5.25 Å2-0 Å2
3----2.01 Å2
Refinement stepCycle: final / Resolution: 2.4→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 0 104 2104
Biso mean---29.81 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132051
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171803
X-RAY DIFFRACTIONr_angle_refined_deg1.621.6422793
X-RAY DIFFRACTIONr_angle_other_deg1.3391.5684198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3095267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.04621.75397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81515305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6521513
X-RAY DIFFRACTIONr_chiral_restr0.0750.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
LS refinement shellResolution: 2.4→2.46 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.432 47 -
Rwork0.256 785 -
obs--90.53 %

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