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- PDB-5zrr: Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R2... -

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Basic information

Entry
Database: PDB / ID: 5zrr
TitleCrystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in monoethyl succinate bound state
ComponentsAlpha/beta hydrolase family protein
KeywordsHYDROLASE / POLYESTERASE / ALPHA/BETA-HYDROLASE FOLD / PROTEIN ENGINEERING / THERMOSTABILITY
Function / homology
Function and homology information


cutinase / carboxylic ester hydrolase activity / metal ion binding
Similarity search - Function
Platelet-activating factor acetylhydrolase, isoform II / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-ethoxy-4-oxobutanoic acid / cutinase
Similarity search - Component
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsNumoto, N. / Kamiya, N. / Bekker, G.J. / Yamagami, Y. / Inaba, S. / Ishii, K. / Uchiyama, S. / Kawai, F. / Ito, N. / Oda, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
CitationJournal: Biochemistry / Year: 2018
Title: Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle.
Authors: Numoto, N. / Kamiya, N. / Bekker, G.J. / Yamagami, Y. / Inaba, S. / Ishii, K. / Uchiyama, S. / Kawai, F. / Ito, N. / Oda, M.
History
DepositionApr 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8068
Polymers29,2101
Non-polymers5967
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-120 kcal/mol
Surface area10750 Å2
Unit cell
Length a, b, c (Å)49.507, 61.397, 76.783
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha/beta hydrolase family protein / Cutinase


Mass: 29209.658 Da / Num. of mol.: 1 / Mutation: S176A, S226P, R228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Gene: Cut190, SAMN02982918_2340 / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) / References: UniProt: W0TJ64

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Non-polymers , 5 types, 283 molecules

#2: Chemical ChemComp-9J3 / 4-ethoxy-4-oxobutanoic acid


Mass: 146.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.01 M ZnSO4, 0.1 M MES pH 6.5, 25% v/v PEG MME 550

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 3, 2016
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.34→50 Å / Num. obs: 52202 / % possible obs: 97.7 % / Redundancy: 6.1 % / Biso Wilson estimate: 7.43492780712 Å2 / CC1/2: 0.998 / Rsym value: 0.096 / Net I/σ(I): 14.5
Reflection shellResolution: 1.34→1.42 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7351 / CC1/2: 0.808 / Rsym value: 0.401 / % possible all: 86.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WFI

4wfi


Resolution: 1.34→41.6080737773 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38102746862
RfactorNum. reflection% reflectionSelection details
Rfree0.185078889065 2614 5.00785470708 %Random selection
Rwork0.162468576973 ---
obs0.163612994953 52198 97.7307620296 %-
Displacement parametersBiso mean: 10.4191268478 Å2
Refinement stepCycle: LAST / Resolution: 1.34→41.6080737773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 25 276 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005964787494352131
X-RAY DIFFRACTIONf_angle_d1.167095405992903
X-RAY DIFFRACTIONf_chiral_restr0.082214089226309
X-RAY DIFFRACTIONf_plane_restr0.00617938823334385
X-RAY DIFFRACTIONf_dihedral_angle_d11.3234708846790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3386-1.3630.409866565191920.3462763134721681X-RAY DIFFRACTION64.7789550603
1.363-1.38920.3231981324121300.3460433210492489X-RAY DIFFRACTION95.0290275762
1.3892-1.41750.3204707410261430.2999313049242627X-RAY DIFFRACTION99.0701001431
1.4175-1.44840.261831636011400.2222236565082634X-RAY DIFFRACTION99.2486583184
1.4484-1.48210.2058180747661320.1762906334472604X-RAY DIFFRACTION99.5995631598
1.4821-1.51910.1916118342211350.1559495938842630X-RAY DIFFRACTION99.6755587599
1.5191-1.56020.1795255958781380.1542440805452644X-RAY DIFFRACTION99.6418338109
1.5602-1.60610.1705415348511420.1523410538922659X-RAY DIFFRACTION99.8218104063
1.6061-1.65790.1807200180091380.1481555425612640X-RAY DIFFRACTION99.928057554
1.6579-1.71720.1865867652011450.1549080508962646X-RAY DIFFRACTION99.9641833811
1.7172-1.7860.1440419329191370.1455313993172658X-RAY DIFFRACTION99.9642346209
1.786-1.86720.1973957128631350.1411430785422660X-RAY DIFFRACTION100
1.8672-1.96570.1647730642061460.1437734314212671X-RAY DIFFRACTION99.9645138396
1.9657-2.08880.1723504721981360.1376985984062663X-RAY DIFFRACTION99.9642857143
2.0888-2.25010.167997904151490.1435767144942692X-RAY DIFFRACTION99.9648135116
2.2501-2.47650.1786443817981410.1466455966622684X-RAY DIFFRACTION99.9292536258
2.4765-2.83480.1991581245241420.1480408166452709X-RAY DIFFRACTION99.9649368864
2.8348-3.57130.139895682421440.1479707227872740X-RAY DIFFRACTION100
3.5713-41.62820.1732549197831490.1647640850092853X-RAY DIFFRACTION99.3710691824

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