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- PDB-7dzv: Cyrstal structure of PETase E186A mutant from Rhizobacter gummiphilus -

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Basic information

Entry
Database: PDB / ID: 7dzv
TitleCyrstal structure of PETase E186A mutant from Rhizobacter gummiphilus
ComponentsDLH domain-containing protein
KeywordsHYDROLASE / PET hydrolase
Function / homologyCutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / extracellular region / PET hydrolase/cutinase-like domain-containing protein
Function and homology information
Biological speciesRhizobacter gummiphilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DLH domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6633
Polymers28,4791
Non-polymers1842
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-1 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.988, 54.627, 108.887
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: 28478.676 Da / Num. of mol.: 1 / Fragment: PET hydrolase / Mutation: E186A
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.66 Å3/Da / Density % sol: 53.8 % / Mosaicity: 0.647 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 7 / Details: Sodium citrate tribasic, Tris, NaCl

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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: 1.6→50 Å / Num. obs: 40798 / % possible obs: 99.4 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Rrim(I) all: 0.1 / Χ2: 3.097 / Net I/σ(I): 14.2 / Num. measured all: 505354
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6312.90.36519780.9850.1030.3792.24597.5
1.63-1.6612.80.33519910.9860.0940.3482.33198.6
1.66-1.6912.80.34319560.9850.0960.3562.36799
1.69-1.7212.70.29320050.990.0830.3052.47697.7
1.72-1.7612.60.25420030.9920.0720.2652.55699
1.76-1.812.60.24220070.9920.0680.2522.60999.5
1.8-1.8512.50.22220230.9890.0630.2312.70799.8
1.85-1.912.40.18820080.9930.0540.1952.85799.3
1.9-1.9512.50.16720250.9940.0480.1742.96799.5
1.95-2.0212.50.14520280.9950.0420.1513.20199.6
2.02-2.0912.30.13220270.9960.0380.1373.32299.8
2.09-2.1712.30.1220180.9950.0350.1263.42599.5
2.17-2.2712.20.10820730.9970.0310.1123.47399.8
2.27-2.3912.20.10120310.9970.0290.1053.54399.8
2.39-2.5412.30.09420580.9970.0270.0983.53399.8
2.54-2.7412.40.08320580.9980.0240.0873.56299.9
2.74-3.0112.60.07420870.9980.0210.0773.564100
3.01-3.4512.70.06720720.9980.020.073.778100
3.45-4.34120.05921150.9980.0180.0623.817100
4.34-5010.70.05722350.9980.0190.063.63899.2

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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: 1.6→30.25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.939 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1571 2057 5 %RANDOM
Rwork0.1329 ---
obs0.1341 38676 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.08 Å2 / Biso mean: 12.936 Å2 / Biso min: 2.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0 Å2
2--1.56 Å20 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 1.6→30.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 0 12 307 2319
Biso mean--30.04 27.83 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132061
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171822
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.6422802
X-RAY DIFFRACTIONr_angle_other_deg1.6851.574242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.465267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36221.66796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.30215307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5721513
X-RAY DIFFRACTIONr_chiral_restr0.1190.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022350
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02437
LS refinement shellResolution: 1.6→1.639 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.172 150 -
Rwork0.15 2680 -
obs--94.24 %

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