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- PDB-6aid: Structural insights into the unique polylactate degrading mechani... -

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Basic information

Entry
Database: PDB / ID: 6aid
TitleStructural insights into the unique polylactate degrading mechanism of Thermobifida alba cutinase
ComponentsEsterase
KeywordsHYDROLASE
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / cutinase activity / cutinase / periplasmic space / extracellular region / metal ion binding
Similarity search - Function
Cutinase / Serine aminopeptidase, S33 / Serine aminopeptidase, S33 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ethyl (2R)-2-oxidanylpropanoate / LACTIC ACID / Cutinase est2
Similarity search - Component
Biological speciesThermobifida alba (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.3 Å
AuthorsKitadokoro, K. / Kakara, M. / Matsui, S. / Osokoshi, R. / Thumarat, U. / Kawai, F. / Kamitani, S.
CitationJournal: Febs J. / Year: 2019
Title: Structural insights into the unique polylactate-degrading mechanism of Thermobifida alba cutinase.
Authors: Kitadokoro, K. / Kakara, M. / Matsui, S. / Osokoshi, R. / Thumarat, U. / Kawai, F. / Kamitani, S.
History
DepositionAug 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7528
Polymers30,3781
Non-polymers3747
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-13 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.265, 68.860, 78.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Esterase /


Mass: 30377.848 Da / Num. of mol.: 1 / Fragment: UNP residues 35-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida alba (bacteria) / Gene: est2 / Production host: Escherichia coli (E. coli) / References: UniProt: F7IX06

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Non-polymers , 5 types, 229 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-9YL / ethyl (2R)-2-oxidanylpropanoate / Ethyl lactate / Ethyl lactate


Mass: 118.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-LAC / LACTIC ACID / Lactic acid


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.89 Å3/Da / Density % sol: 34.91 % / Description: plate like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15-20% (w/v) PEG 3350, 0.2 M sodium acetate, 0.2M2 M calcium chloride, and 0.1 M sodium chloride, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 106239 / % possible obs: 97.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Net I/σ(I): 7.41
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 1.89 % / Mean I/σ(I) obs: 0.91 / Num. unique obs: 17556 / CC1/2: 0.37 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 1.3→50 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.786 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.16465 2790 5 %RANDOM
Rwork0.1329 ---
obs0.13451 53071 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.258 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2---0.15 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 19 222 2250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192073
X-RAY DIFFRACTIONr_bond_other_d0.0030.021907
X-RAY DIFFRACTIONr_angle_refined_deg2.4431.9572821
X-RAY DIFFRACTIONr_angle_other_deg1.25134387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25922.74791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.80815312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8811518
X-RAY DIFFRACTIONr_chiral_restr0.1670.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212361
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02483
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9520.3361043
X-RAY DIFFRACTIONr_mcbond_other0.9510.3331042
X-RAY DIFFRACTIONr_mcangle_it1.2150.5051302
X-RAY DIFFRACTIONr_mcangle_other1.2150.5081303
X-RAY DIFFRACTIONr_scbond_it1.9670.5891030
X-RAY DIFFRACTIONr_scbond_other1.9710.5911031
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2490.7981520
X-RAY DIFFRACTIONr_long_range_B_refined2.3186.0692427
X-RAY DIFFRACTIONr_long_range_B_other2.326.0912428
X-RAY DIFFRACTIONr_rigid_bond_restr6.0233980
X-RAY DIFFRACTIONr_sphericity_free16.9695125
X-RAY DIFFRACTIONr_sphericity_bonded4.76754032
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 178 -
Rwork0.365 3245 -
obs--82.56 %
Refinement TLS params.

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)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3525-0.0305-0.07550.3048-0.01290.45310.0120.0020.02740.00260.012-0.0017-0.0136-0.0026-0.02390.0492-0.0030.00220.0745-0.00320.06461.9999-3.675511.8091
20000000000000000.02940.0560.03290.15050.03040.061-17.0338-1.19324.8988
30000000000000000.0348-0.018-0.01110.0682-0.01310.069-1.084-19.0567-0.282
40000000000000000.05530.0158-0.0060.06-0.02230.077219.3838-16.601714.5874
50.3883-0.0812-0.04970.3473-0.06860.33830.01910.00930.02-0.01590.01560.00960.0077-0.0168-0.03470.0194-0.00750.00010.04450.00120.03991.1601-4.02088.9585
616.50728.1381-1.900210.69522.2991.7855-0.44790.21030.2119-0.0730.15680.75480.12280.00290.29110.05810.01210.00380.09810.02380.08291.7202-13.174324.9539
71.50820.8345-1.66220.5021-0.93461.83760.0177-0.030.00760.0109-0.01080.0086-0.01660.0345-0.00690.07190.00560.01240.09280.00680.1029-4.3545-1.72926.9348
839.88130.3904-69.0348265.66081.067131.3804-0.0902-0.7215-0.74532.0993-1.1051-1.00590.63631.12371.19540.04460.0638-0.04870.1942-0.11010.1014.2384-9.931330.3635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 300
2X-RAY DIFFRACTION2A401
3X-RAY DIFFRACTION3A402
4X-RAY DIFFRACTION4A403
5X-RAY DIFFRACTION5A501 - 722
6X-RAY DIFFRACTION6A404
7X-RAY DIFFRACTION7A405 - 406
8X-RAY DIFFRACTION8A407

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