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- PDB-8bra: Polyester Hydrolase Leipzig 7 (PHL7) bound to terephthalic acid (... -

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Basic information

Entry
Database: PDB / ID: 8bra
TitlePolyester Hydrolase Leipzig 7 (PHL7) bound to terephthalic acid (TPA) and Mg2+
ComponentsPolyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
KeywordsHYDROLASE / PETase / Cutinase / Polyethylene terephthalate / terephthalic acid / TPA / polyester hydrolase / Mg2+ / magnesium
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 20, 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)58,2955
Polymers58,0812
Non-polymers2153
Water14,988832
1
A: Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0652
Polymers29,0401
Non-polymers241
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)29,2313
Polymers29,0401
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.352, 56.069, 100.442
Angle α, β, γ (deg.)90.00, 94.01, 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
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UB7 / terephthalic acid / benzene-1,4-dicarboxylic acid


Mass: 166.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 832 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50 mM Tris 100 mM KCl 30 % (v/v) PEG 400 10 mM MgCl2

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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: May 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.7→21.46 Å / Num. obs: 63959 / % possible obs: 99.77 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.05707 / Rpim(I) all: 0.02696 / Rrim(I) all: 0.06349 / Net I/σ(I): 19.81
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.3389 / Mean I/σ(I) obs: 3.02 / Num. unique obs: 6341 / CC1/2: 0.838 / Rpim(I) all: 0.2168 / Rrim(I) all: 0.4043 / % possible all: 99.83

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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→21.46 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1605 2885 4.51 %copied from PDB ID: 7NEI
Rwork0.1295 ---
obs0.1309 63957 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→21.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 14 832 4782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084127
X-RAY DIFFRACTIONf_angle_d0.9565654
X-RAY DIFFRACTIONf_dihedral_angle_d12.4341513
X-RAY DIFFRACTIONf_chiral_restr0.056631
X-RAY DIFFRACTIONf_plane_restr0.012762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.21731520.17532823X-RAY DIFFRACTION100
1.73-1.760.20871490.16992902X-RAY DIFFRACTION100
1.76-1.790.1861690.16392884X-RAY DIFFRACTION100
1.79-1.820.20921270.15392904X-RAY DIFFRACTION100
1.82-1.860.16791360.14762909X-RAY DIFFRACTION100
1.86-1.90.181130.14672886X-RAY DIFFRACTION100
1.9-1.950.21081090.13962943X-RAY DIFFRACTION100
1.95-1.990.17141400.13632869X-RAY DIFFRACTION100
1.99-2.050.17461360.12982913X-RAY DIFFRACTION100
2.05-2.110.16561760.12982849X-RAY DIFFRACTION100
2.11-2.180.17071270.12442928X-RAY DIFFRACTION100
2.18-2.250.14051250.12072929X-RAY DIFFRACTION100
2.25-2.340.15991070.11852917X-RAY DIFFRACTION100
2.34-2.450.1511370.1162890X-RAY DIFFRACTION100
2.45-2.580.13981300.11892918X-RAY DIFFRACTION100
2.58-2.740.14611390.11932921X-RAY DIFFRACTION100
2.74-2.950.14261350.12592906X-RAY DIFFRACTION100
2.95-3.250.18061370.13082900X-RAY DIFFRACTION100
3.25-3.720.16081410.1252943X-RAY DIFFRACTION100
3.72-4.670.12831340.10882942X-RAY DIFFRACTION100
4.68-21.460.1451660.14052996X-RAY DIFFRACTION100
Refinement TLS params.

T23: -0.002 Å2 / 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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4273-0.0461-0.00931.2569-0.45950.7514-0.01140.00270.0062-0.02840.04170.12870.0079-0.08780.01440.03750.0052-0.00930.06230.051713.13163.158242.8477
20.55440.0547-0.04071.1221-0.41850.8711-0.0092-0.02090.0142-0.05960.02720.0830.041-0.06640.01120.0419-0.00580.00450.04820.034916.6536-4.68787.137
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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