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- PDB-7nei: Polyester Hydrolase Leipzig 7 (PHL7) in the unliganded state -

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Basic information

Entry
Database: PDB / ID: 7nei
TitlePolyester Hydrolase Leipzig 7 (PHL7) in the unliganded state
ComponentsPolyester Hydrolase Leipzig 7 (PHL-7)
KeywordsHYDROLASE / PETase / Cutinase / Polyethylene terephthalate
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsRichter, P.K. / Strater, N.
CitationJournal: ChemSusChem / Year: 2022
Title: Low Carbon Footprint Recycling of Post-Consumer PET Plastic with a Metagenomic Polyester Hydrolase.
Authors: Sonnendecker, C. / Oeser, J. / Richter, P.K. / Hille, P. / Zhao, Z. / Fischer, C. / Lippold, H. / Blazquez-Sanchez, P. / Engelberger, F. / Ramirez-Sarmiento, C.A. / Oeser, T. / Lihanova, Y. ...Authors: Sonnendecker, C. / Oeser, J. / Richter, P.K. / Hille, P. / Zhao, Z. / Fischer, C. / Lippold, H. / Blazquez-Sanchez, P. / Engelberger, F. / Ramirez-Sarmiento, C.A. / Oeser, T. / Lihanova, Y. / Frank, R. / Jahnke, H.G. / Billig, S. / Abel, B. / Strater, N. / Matysik, J. / Zimmermann, W.
History
DepositionFeb 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Nov 23, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyester Hydrolase Leipzig 7 (PHL-7)
B: Polyester Hydrolase Leipzig 7 (PHL-7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1594
Polymers58,1132
Non-polymers462
Water15,349852
1
A: Polyester Hydrolase Leipzig 7 (PHL-7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0792
Polymers29,0561
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polyester Hydrolase Leipzig 7 (PHL-7)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0792
Polymers29,0561
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.350, 97.680, 101.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 9 or resid 11...
d_2ens_1(chain "B" and (resid 2 through 9 or resid 11...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAPROA1 - 8
d_12ens_1PROTHRA12 - 13
d_13ens_1SERALAA19 - 22
d_14ens_1ARGALAA24 - 28
d_15ens_1ALAALAA32 - 41
d_16ens_1GLYGLYA45 - 74
d_17ens_1GLUGLUA78
d_18ens_1ILEGLYA80 - 110
d_19ens_1GLNASNA112 - 123
d_110ens_1VALARGA125 - 134
d_111ens_1ALAHISA138 - 142
d_112ens_1METLEUA146 - 152
d_113ens_1ALATHRA156 - 161
d_114ens_1LEUTHRA165 - 176
d_115ens_1LYSLYSA180
d_116ens_1TRPPROA182 - 214
d_117ens_1ASPTYRA218 - 223
d_118ens_1GLUASNA227 - 237
d_119ens_1PROASPA239 - 270
d_120ens_1PHEALAA272 - 273
d_121ens_1SERSERA277
d_122ens_1ARGPHEA284 - 289
d_21ens_1ALAPROC1 - 8
d_22ens_1PROTHRC10 - 11
d_23ens_1SERALAC18 - 21
d_24ens_1ARGALAC25 - 29
d_25ens_1ALAALAC33 - 42
d_26ens_1GLYGLYC46 - 75
d_27ens_1GLUGLUC77
d_28ens_1ILEGLYC81 - 111
d_29ens_1GLNASNC115 - 126
d_210ens_1VALARGC131 - 140
d_211ens_1ALAHISC144 - 148
d_212ens_1METLEUC152 - 158
d_213ens_1ALATHRC162 - 167
d_214ens_1LEUTHRC169 - 180
d_215ens_1LYSLYSC182
d_216ens_1TRPPROC186 - 218
d_217ens_1ASPTYRC220 - 225
d_218ens_1GLUASNC229 - 239
d_219ens_1PROASPC243 - 274
d_220ens_1PHEPHEC277
d_221ens_1ALAALAC280
d_222ens_1SERSERC284
d_223ens_1ARGPHEC289 - 294

NCS oper: (Code: givenMatrix: (-0.999992023971, -0.00269336690579, -0.00294919800375), (-0.00293486802642, 0.996359197138, 0.085204089268), (0.00270897468095, 0.0852120651847, -0.996359154825)Vector: ...NCS oper: (Code: given
Matrix: (-0.999992023971, -0.00269336690579, -0.00294919800375), (-0.00293486802642, 0.996359197138, 0.085204089268), (0.00270897468095, 0.0852120651847, -0.996359154825)
Vector: 56.2477289988, 4.38350856439, -53.9374882301)

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Components

#1: Protein Polyester Hydrolase Leipzig 7 (PHL-7)


Mass: 29056.262 Da / Num. of mol.: 2
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 852 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM sodium citrate 20 % (w/v) PEG 4,000 20 % (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.3→56.35 Å / Num. obs: 127681 / % possible obs: 93 % / Redundancy: 12.1 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Rrim(I) all: 0.073 / Net I/σ(I): 18.9 / Num. measured all: 1548512 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.3-1.3271.40437540.5510.5651.5256.5
7.12-49.21911.90.0279560.9990.0080.02899.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
MxCuBEdata collection
XDS20200417data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 1.3→49.22 Å / SU ML: 0.1159 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1594 6202 4.86 %
Rwork0.1316 121375 -
obs0.133 127577 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.55 Å2
Refinement stepCycle: LAST / Resolution: 1.3→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 0 2 852 4774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614204
X-RAY DIFFRACTIONf_angle_d0.93615785
X-RAY DIFFRACTIONf_chiral_restr0.0778649
X-RAY DIFFRACTIONf_plane_restr0.007772
X-RAY DIFFRACTIONf_dihedral_angle_d26.16261565
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.617492344085 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.31231240.26182360X-RAY DIFFRACTION54.21
1.31-1.330.26971480.25382558X-RAY DIFFRACTION60
1.33-1.350.26931680.23722833X-RAY DIFFRACTION66.15
1.35-1.360.26641610.22683118X-RAY DIFFRACTION72.43
1.36-1.380.26631330.21633310X-RAY DIFFRACTION76.05
1.38-1.40.26521660.20633588X-RAY DIFFRACTION82.91
1.4-1.420.23192020.20383810X-RAY DIFFRACTION88.04
1.42-1.440.23461840.18334029X-RAY DIFFRACTION92.88
1.44-1.460.21411980.16784168X-RAY DIFFRACTION95.77
1.46-1.490.2152060.15754231X-RAY DIFFRACTION98.12
1.49-1.510.18442170.13884329X-RAY DIFFRACTION99.78
1.51-1.540.16522420.13064288X-RAY DIFFRACTION99.96
1.54-1.570.17242090.12694302X-RAY DIFFRACTION99.6
1.57-1.60.15792240.12214314X-RAY DIFFRACTION99.69
1.6-1.640.1481950.12044370X-RAY DIFFRACTION100
1.64-1.680.16172370.12154325X-RAY DIFFRACTION99.98
1.68-1.720.14172280.12214313X-RAY DIFFRACTION99.34
1.72-1.760.17812030.1274358X-RAY DIFFRACTION100
1.76-1.820.15242360.12414341X-RAY DIFFRACTION100
1.82-1.870.16382380.12344334X-RAY DIFFRACTION99.61
1.87-1.940.15792290.12174345X-RAY DIFFRACTION99.98
1.94-2.020.14832220.12374334X-RAY DIFFRACTION99.58
2.02-2.110.1522340.12594319X-RAY DIFFRACTION99.78
2.11-2.220.13742740.11554335X-RAY DIFFRACTION99.72
2.22-2.360.13692030.1144396X-RAY DIFFRACTION99.76
2.36-2.540.15131990.11244400X-RAY DIFFRACTION99.89
2.54-2.80.12732420.12074411X-RAY DIFFRACTION99.91
2.8-3.210.14991810.12754448X-RAY DIFFRACTION99.63
3.21-4.040.16812350.13014491X-RAY DIFFRACTION99.83
4.04-49.220.14562640.13474617X-RAY DIFFRACTION99.45

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