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- PDB-8brb: Polyester Hydrolase Leipzig 7 (PHL7) bound to terephthalic acid (TPA) -

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Basic information

Entry
Database: PDB / ID: 8brb
TitlePolyester Hydrolase Leipzig 7 (PHL7) bound to terephthalic acid (TPA)
ComponentsPolyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
KeywordsHYDROLASE / PETase / Cutinase / Polyethylene terephthalate / terephthalic acid / TPA / polyester hydrolase
Function / homologyterephthalic acid
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsRichter, P.K. / Strater, N.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)358304989 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Structure and function of the metagenomic plastic-degrading polyester hydrolase PHL7 bound to its product.
Authors: Richter, P.K. / Blazquez-Sanchez, P. / Zhao, Z. / Engelberger, F. / Wiebeler, C. / Kunze, G. / Frank, R. / Krinke, D. / Frezzotti, E. / Lihanova, Y. / Falkenstein, P. / Matysik, J. / ...Authors: Richter, P.K. / Blazquez-Sanchez, P. / Zhao, Z. / Engelberger, F. / Wiebeler, C. / Kunze, G. / Frank, R. / Krinke, D. / Frezzotti, E. / Lihanova, Y. / Falkenstein, P. / Matysik, J. / Zimmermann, W. / Strater, N. / Sonnendecker, C.
History
DepositionNov 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Author supporting evidence / Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.2Nov 6, 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: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
B: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5696
Polymers58,0812
Non-polymers4894
Water16,394910
1
A: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2853
Polymers29,0401
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2853
Polymers29,0401
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.912, 56.510, 101.744
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant


Mass: 29040.262 Da / Num. of mol.: 2 / Mutation: S131A
Source method: isolated from a genetically manipulated source
Details: metagenomic analysis / Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-UB7 / terephthalic acid / benzene-1,4-dicarboxylic acid


Mass: 166.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM sodium citrate 20 % (w/v) PEG 4,000 5 % (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.5406 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.7→21.57 Å / Num. obs: 66097 / % possible obs: 99.84 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07515 / Rpim(I) all: 0.0303 / Rrim(I) all: 0.08131 / Net I/σ(I): 18.33
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4792 / Num. unique obs: 6614 / CC1/2: 0.832 / Rpim(I) all: 0.2392 / Rrim(I) all: 0.537 / % possible all: 99.97

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Processing

Software
NameVersionClassification
PHENIX1.2refinement
CrysalisPro171.41.112adata collection
CrysalisPro171.41.112adata reduction
Aimless0.7.7data scaling
Coot0.9.2model building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7NEI

7nei


Resolution: 1.7→21.57 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 2978 4.51 %copied from PDB ID: 7NEI
Rwork0.16 ---
obs0.162 66048 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.27 Å2
Refinement stepCycle: LAST / Resolution: 1.7→21.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3933 0 32 910 4875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044181
X-RAY DIFFRACTIONf_angle_d0.7735731
X-RAY DIFFRACTIONf_dihedral_angle_d12.0211540
X-RAY DIFFRACTIONf_chiral_restr0.048634
X-RAY DIFFRACTIONf_plane_restr0.009781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.2291420.19672980X-RAY DIFFRACTION100
1.73-1.760.271670.19773009X-RAY DIFFRACTION100
1.76-1.790.24121590.19292930X-RAY DIFFRACTION100
1.79-1.820.21881630.18512971X-RAY DIFFRACTION100
1.82-1.860.25461210.18112989X-RAY DIFFRACTION100
1.86-1.90.26021250.22893018X-RAY DIFFRACTION100
1.9-1.950.28841190.23433030X-RAY DIFFRACTION100
1.95-1.990.21131370.17432962X-RAY DIFFRACTION100
1.99-2.050.21781360.1573018X-RAY DIFFRACTION100
2.05-2.110.20981580.15472983X-RAY DIFFRACTION100
2.11-2.180.19361620.14692962X-RAY DIFFRACTION100
2.18-2.250.25571260.19752993X-RAY DIFFRACTION99
2.25-2.340.241060.18463019X-RAY DIFFRACTION100
2.34-2.450.20671440.1493005X-RAY DIFFRACTION100
2.45-2.580.19661420.14493002X-RAY DIFFRACTION100
2.58-2.740.19161280.13743002X-RAY DIFFRACTION100
2.74-2.950.18011500.14583021X-RAY DIFFRACTION100
2.95-3.250.2091460.15133010X-RAY DIFFRACTION100
3.25-3.720.18581360.1433036X-RAY DIFFRACTION100
3.72-4.670.17551410.12883040X-RAY DIFFRACTION100
4.68-21.570.17831700.15593090X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5283-0.0874-0.02480.8441-0.30820.89710.0088-0.0087-0.01540.0560.0090.00160.0174-0.12830.05190.0674-0.0128-0.01870.09490.00080.063413.2033.418743.6593
20.9430.16970.08150.6374-0.10180.68670.0105-0.0959-0.0018-0.0881-0.0124-0.04410.0333-0.0502-0.05210.05470.00150.02250.0546-0.00180.059916.8424-5.04487.0768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 260)
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 260)

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