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- PDB-8d1d: PROSS PETase -

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Basic information

Entry
Database: PDB / ID: 8d1d
TitlePROSS PETase
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / plastic
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsVongsouthi, V. / Jackson, C.J. / Tan, L.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: PROSS PETase
Authors: Vongsouthi, V. / Jackson, C.J. / Tan, L.
History
DepositionMay 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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: Poly(ethylene terephthalate) hydrolase
C: Poly(ethylene terephthalate) hydrolase
E: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2725
Polymers83,1923
Non-polymers802
Water7,981443
1
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7712
Polymers27,7311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7712
Polymers27,7311
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)27,7311
Polymers27,7311
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.586, 159.173, 45.043
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-301-

CA

21A-585-

HOH

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase


Mass: 27730.684 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: PROSS PETase / Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.94 Å3/Da / Density % sol: 58.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 20% v/v glycerol, 0.08 M sodium cacodylate, 14.4% w/v PEG 8K, 0.16M calcium acetate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.42→45.04 Å / Num. obs: 177110 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 14.63 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.065 / Net I/σ(I): 7.2
Reflection shellResolution: 1.42→1.45 Å / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 8075 / CC1/2: 0.542

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJH

5xjh


Resolution: 1.42→39.79 Å / SU ML: 0.1899 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.2294
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2339 8959 5.06 %
Rwork0.198 168051 -
obs0.1999 177010 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.08 Å2
Refinement stepCycle: LAST / Resolution: 1.42→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5747 0 2 443 6192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00786060
X-RAY DIFFRACTIONf_angle_d0.94578274
X-RAY DIFFRACTIONf_chiral_restr0.0775905
X-RAY DIFFRACTIONf_plane_restr0.00751105
X-RAY DIFFRACTIONf_dihedral_angle_d12.38952154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.36282810.31925235X-RAY DIFFRACTION91.95
1.44-1.460.30863100.23735478X-RAY DIFFRACTION96.77
1.46-1.470.27912900.22195563X-RAY DIFFRACTION99
1.47-1.490.26672450.21345546X-RAY DIFFRACTION97.28
1.49-1.510.25892860.20175572X-RAY DIFFRACTION97.93
1.51-1.530.27543240.19365533X-RAY DIFFRACTION98.77
1.53-1.550.23922900.1845525X-RAY DIFFRACTION96.85
1.55-1.580.23762860.18415602X-RAY DIFFRACTION99.43
1.58-1.60.25072920.19865608X-RAY DIFFRACTION97.8
1.6-1.630.27093220.19885558X-RAY DIFFRACTION98.87
1.63-1.660.25382860.17575574X-RAY DIFFRACTION98.67
1.66-1.690.21492840.17385597X-RAY DIFFRACTION98.41
1.69-1.720.23293220.17515568X-RAY DIFFRACTION99.12
1.72-1.750.22793090.16885609X-RAY DIFFRACTION98.55
1.75-1.790.22273210.17055566X-RAY DIFFRACTION99.09
1.79-1.830.23993120.17715586X-RAY DIFFRACTION99.08
1.83-1.880.2353110.17235641X-RAY DIFFRACTION98.62
1.88-1.930.21472970.17935601X-RAY DIFFRACTION99.93
1.93-1.990.23853370.18695610X-RAY DIFFRACTION99.07
1.99-2.050.25793080.19815624X-RAY DIFFRACTION99.33
2.05-2.130.23692760.20025696X-RAY DIFFRACTION99.87
2.13-2.210.23992840.19595638X-RAY DIFFRACTION99.5
2.21-2.310.23472830.19585677X-RAY DIFFRACTION99.6
2.31-2.430.22323450.19365625X-RAY DIFFRACTION99.63
2.43-2.590.21313140.19545657X-RAY DIFFRACTION99.88
2.59-2.780.24642750.20045717X-RAY DIFFRACTION99.95
2.78-3.060.23142990.2095693X-RAY DIFFRACTION99.95
3.06-3.510.22982780.21165702X-RAY DIFFRACTION99.98
3.51-4.420.21732890.20175713X-RAY DIFFRACTION99.87
4.42-39.790.21733030.20845737X-RAY DIFFRACTION99.54

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