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- PDB-6scd: Polyester hydrolase PE-H Y250S mutant of Pseudomonas aestusnigri -

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Basic information

Entry
Database: PDB / ID: 6scd
TitlePolyester hydrolase PE-H Y250S mutant of Pseudomonas aestusnigri
ComponentsPolyester hydrolase
KeywordsHYDROLASE / polyester degradation / PET hydrolase / marine bacteria / Pseudomonas aestusnigri
Function / homology
Function and homology information


Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / DLH domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aestusnigri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBollinger, A. / Thies, S. / Kobus, S. / Hoeppner, A. / Smits, S.H.J. / Jaeger, K.-E.
CitationJournal: Front Microbiol / Year: 2020
Title: A Novel Polyester Hydrolase From the Marine BacteriumPseudomonas aestusnigri -Structural and Functional Insights.
Authors: Bollinger, A. / Thies, S. / Knieps-Grunhagen, E. / Gertzen, C. / Kobus, S. / Hoppner, A. / Ferrer, M. / Gohlke, H. / Smits, S.H.J. / Jaeger, K.E.
History
DepositionJul 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyester hydrolase
B: Polyester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,56416
Polymers66,6582
Non-polymers90614
Water8,881493
1
A: Polyester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,05811
Polymers33,3291
Non-polymers72910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5055
Polymers33,3291
Non-polymers1764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.526, 98.268, 121.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Polyester hydrolase


Mass: 33329.047 Da / Num. of mol.: 2 / Mutation: Y250S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aestusnigri (bacteria) / Gene: B7O88_11480 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1H6AD45

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Non-polymers , 8 types, 507 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 493 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulphate, 0.1 M sodium citrate pH 3.5, 28 % (v/v) PEG 400

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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: P13 (MX1) / Wavelength: 0.9505 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9505 Å / Relative weight: 1
ReflectionResolution: 1.35→77 Å / Num. obs: 122029 / % possible obs: 99.1 % / Redundancy: 4.05 % / Rsym value: 0.043 / Net I/σ(I): 14.98
Reflection shellResolution: 1.35→1.42 Å / Num. unique obs: 19634 / Rsym value: 0.439

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SBN

6sbn


Resolution: 1.35→76.34 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.536 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.042
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1517 6011 4.9 %RANDOM
Rwork0.1127 ---
obs0.1146 116011 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.37 Å2 / Biso mean: 21.684 Å2 / Biso min: 5.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 1.35→76.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3995 0 49 493 4537
Biso mean--33.01 35.55 -
Num. residues----532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0194203
X-RAY DIFFRACTIONr_bond_other_d0.0020.023770
X-RAY DIFFRACTIONr_angle_refined_deg2.431.9515736
X-RAY DIFFRACTIONr_angle_other_deg1.33638707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.81323.353173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2215620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.411526
X-RAY DIFFRACTIONr_chiral_restr0.1490.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0214866
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02988
X-RAY DIFFRACTIONr_rigid_bond_restr5.79937972
X-RAY DIFFRACTIONr_sphericity_free39.3525155
X-RAY DIFFRACTIONr_sphericity_bonded15.36758206
LS refinement shellResolution: 1.351→1.386 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 417 -
Rwork0.2 8523 -
all-8940 -
obs--99.12 %

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