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

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Basic information

Entry
Database: PDB / ID: 5zno
TitleCrystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S/ mutant in Ca(2+)-bound state
ComponentsAlpha/beta hydrolase family protein
KeywordsHYDROLASE / POLYESTERASE / ALPHA/BETA-HYDROLASE FOLD / PROTEIN ENGINEERING / THERMOSTABILITY
Function / homology
Function and homology information


carboxylic ester hydrolase activity / metal ion binding
Similarity search - Function
Platelet-activating factor acetylhydrolase, isoform II / Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.60264346898 Å
AuthorsNumoto, N. / Inaba, S. / Yamagami, Y. / Kamiya, N. / Bekker, G.J. / Ishii, K. / Uchiyama, S. / Kawai, F. / Ito, N. / Oda, M.
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 10, 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
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_asym_id / _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.ptnr3_auth_asym_id / _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.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 / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,12814
Polymers58,3872
Non-polymers74112
Water14,214789
1
A: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5907
Polymers29,1941
Non-polymers3976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5387
Polymers29,1941
Non-polymers3456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.705, 49.732, 95.655
Angle α, β, γ (deg.)90.0, 99.589, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 29193.658 Da / Num. of mol.: 2 / Mutation: S176A, S226P, R228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Strain: AHK190 / Gene: Cut190, SAMN02982918_2340 / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) / References: UniProt: W0TJ64, cutinase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 10% w/v PEG 8000, 8% v/v Ethylene glycol

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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: Dec 9, 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: 1.6→50 Å / Num. obs: 75063 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.4807795741 Å2 / CC1/2: 0.992 / Rsym value: 0.136 / Net I/σ(I): 6.8
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.2 % / Num. unique obs: 12065 / CC1/2: 0.518 / Rsym value: 0.95 / % possible all: 99.3

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Processing

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

4wfj


Resolution: 1.60264346898→47.7178508489 Å / SU ML: 0.235868861104 / Cross valid method: FREE R-VALUE / σ(F): 1.3474730099 / Phase error: 22.9434927349
RfactorNum. reflection% reflectionSelection details
Rfree0.221789713647 3748 4.99420363239 %Random selection
Rwork0.179309456211 ---
obs0.181415484335 75047 99.2501388632 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.919072451 Å2
Refinement stepCycle: LAST / Resolution: 1.60264346898→47.7178508489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 37 789 4876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006816875495244199
X-RAY DIFFRACTIONf_angle_d1.061791220895710
X-RAY DIFFRACTIONf_chiral_restr0.045203961528612
X-RAY DIFFRACTIONf_plane_restr0.00600048610744753
X-RAY DIFFRACTIONf_dihedral_angle_d12.18011576281551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6026-1.62290.3257331900131360.3186938122600X-RAY DIFFRACTION98.4172661871
1.6229-1.64430.3790138177091390.3177299282962637X-RAY DIFFRACTION99.6768402154
1.6443-1.66680.3305272813531400.3303347606462637X-RAY DIFFRACTION99.3915533286
1.6668-1.69060.3482289847371370.3212638364722601X-RAY DIFFRACTION99.5636363636
1.6906-1.71590.3571057168561390.2799533413822655X-RAY DIFFRACTION99.3245645219
1.7159-1.74270.3175323266251370.2715048730852623X-RAY DIFFRACTION99.7470184315
1.7427-1.77120.2849391689951390.2550986934872631X-RAY DIFFRACTION98.9992852037
1.7712-1.80180.2814921212531380.2381232341782605X-RAY DIFFRACTION99.420079739
1.8018-1.83460.2866249855741400.2252243711642642X-RAY DIFFRACTION99.1446899501
1.8346-1.86980.2722660221731380.2221377957812618X-RAY DIFFRACTION99.6384671005
1.8698-1.9080.2795259267531390.2091454331172648X-RAY DIFFRACTION99.8209169054
1.908-1.94950.2614498334011370.2147689758282613X-RAY DIFFRACTION99.2063492063
1.9495-1.99480.2685774149591400.2112421864022653X-RAY DIFFRACTION98.9723600283
1.9948-2.04470.2507940253561380.2007135480032594X-RAY DIFFRACTION99.5264116576
2.0447-2.10.2363113158571370.1883700862732645X-RAY DIFFRACTION99.4992846924
2.1-2.16180.2527883997271400.1855783202082660X-RAY DIFFRACTION99.4318181818
2.1618-2.23160.1992237740871380.1811896480242651X-RAY DIFFRACTION99.4295900178
2.2316-2.31140.2300765187781360.1748917869762622X-RAY DIFFRACTION99.0305206463
2.3114-2.40390.2274555613061390.1612776139712633X-RAY DIFFRACTION99.3548387097
2.4039-2.51330.1987110633841390.1648380119832640X-RAY DIFFRACTION99.3919885551
2.5133-2.64580.1842674249921400.1592629329262657X-RAY DIFFRACTION99.7503566334
2.6458-2.81150.2133213858981390.1598754236682663X-RAY DIFFRACTION99.4322214336
2.8115-3.02860.1869819185031410.1569206581732661X-RAY DIFFRACTION99.3617021277
3.0286-3.33330.1986530387351390.1534096095452656X-RAY DIFFRACTION98.9730878187
3.3333-3.81550.1720988462761380.1364199684082644X-RAY DIFFRACTION98.6175115207
3.8155-4.80640.1648882348071410.1259888688482673X-RAY DIFFRACTION98.426023085
4.8064-47.7390.1752790896351440.1485841753132737X-RAY DIFFRACTION98.3612154319

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