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- PDB-7qjo: Crystal structure of a cutinase enzyme from Marinactinospora ther... -

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Basic information

Entry
Database: PDB / ID: 7qjo
TitleCrystal structure of a cutinase enzyme from Marinactinospora thermotolerans DSM45154 (606)
ComponentsCutinase
KeywordsHYDROLASE / plastic degradation
Function / homologyDienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold / hydrolase activity / Cutinase
Function and homology information
Biological speciesMarinactinospora thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.933 Å
AuthorsZahn, M. / Shakespeare, T.J. / Beckham, G.T. / McGeehan, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)Research England E3 funding United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity
Authors: Erickson, E. / Gado, J.E. / Avilan, L. / Bratti, F. / Brizendine, R.K. / Cox, P.A. / Gill, R. / Graham, R. / Kim, D.J. / Konig, G. / Michener, W.E. / Poudel, S. / Ramirez, K.J. / ...Authors: Erickson, E. / Gado, J.E. / Avilan, L. / Bratti, F. / Brizendine, R.K. / Cox, P.A. / Gill, R. / Graham, R. / Kim, D.J. / Konig, G. / Michener, W.E. / Poudel, S. / Ramirez, K.J. / Shakespeare, T.J. / Zahn, M. / Boyd, E.S. / Payne, C.M. / DuBois, J.L. / Pickford, A.R. / Beckham, G.T. / McGeehan, J.E.
History
DepositionDec 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cutinase
A: Cutinase


Theoretical massNumber of molelcules
Total (without water)59,8302
Polymers59,8302
Non-polymers00
Water4,468248
1
B: Cutinase


Theoretical massNumber of molelcules
Total (without water)29,9151
Polymers29,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cutinase


Theoretical massNumber of molelcules
Total (without water)29,9151
Polymers29,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.966, 45.354, 86.598
Angle α, β, γ (deg.)90.000, 108.193, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 1 - 262 / Label seq-ID: 2 - 263

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11BA
22AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Cutinase /


Mass: 29914.756 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinactinospora thermotolerans (bacteria)
Gene: SAMN02745673_00423 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1T4KK94
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium HEPES pH 7.5, 70% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.933→82.269 Å / Num. obs: 29683 / % possible obs: 91.6 % / Redundancy: 5.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.253 / Rpim(I) all: 0.114 / Net I/σ(I): 5.5
Reflection shellResolution: 1.933→2.097 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.343 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1485 / CC1/2: 0.577 / Rpim(I) all: 0.555 / % possible all: 52

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WFJ

4wfj


Resolution: 1.933→82.269 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.85 / SU B: 12.913 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / ESU R: 0.317 / ESU R Free: 0.241
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.282 1448 4.878 %
Rwork0.2322 28235 -
all0.235 --
obs-29683 71.91 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.851 Å2
Baniso -1Baniso -2Baniso -3
1--0.485 Å20 Å20.121 Å2
2---0.195 Å2-0 Å2
3---0.494 Å2
Refinement stepCycle: LAST / Resolution: 1.933→82.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 0 248 4292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134150
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143646
X-RAY DIFFRACTIONr_angle_refined_deg1.741.6495666
X-RAY DIFFRACTIONr_angle_other_deg1.3421.5758420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3435522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56921.913230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57515604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4851530
X-RAY DIFFRACTIONr_chiral_restr0.0770.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02970
X-RAY DIFFRACTIONr_nbd_refined0.2080.2922
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.23703
X-RAY DIFFRACTIONr_nbtor_refined0.170.22002
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1060.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2980.221
X-RAY DIFFRACTIONr_nbd_other0.3590.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.213
X-RAY DIFFRACTIONr_mcbond_it0.6821.52094
X-RAY DIFFRACTIONr_mcbond_other0.6751.4982093
X-RAY DIFFRACTIONr_mcangle_it1.1552.2442614
X-RAY DIFFRACTIONr_mcangle_other1.1562.2462615
X-RAY DIFFRACTIONr_scbond_it0.7261.5852056
X-RAY DIFFRACTIONr_scbond_other0.7261.5862057
X-RAY DIFFRACTIONr_scangle_it1.2052.3553052
X-RAY DIFFRACTIONr_scangle_other1.2042.3563053
X-RAY DIFFRACTIONr_lrange_it2.85818.0794745
X-RAY DIFFRACTIONr_lrange_other2.79117.9694710
X-RAY DIFFRACTIONr_ncsr_local_group_10.0530.058957
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.052860.0501
12AX-RAY DIFFRACTIONLocal ncs0.052860.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.933-1.9840.42670.265820.27630420.6430.8362.92570.257
1.984-2.0380.321320.2984490.29929080.7090.7716.54060.286
2.038-2.0970.349410.2838700.28628880.7220.76631.54430.271
2.097-2.1610.338620.25511480.25928020.7940.82343.18340.24
2.161-2.2320.294730.26314750.26526830.8110.83757.69660.249
2.232-2.3110.285810.25717930.25926110.8320.83871.77330.239
2.311-2.3980.307940.2619440.26225410.8110.83680.20460.238
2.398-2.4960.3231140.28121080.28324330.7760.78991.32760.255
2.496-2.6060.3151270.28821520.2923240.7750.75398.06370.266
2.606-2.7330.3071080.25721390.2622470.8040.841000.235
2.733-2.8810.306950.23220370.23521320.8550.8931000.206
2.881-3.0560.2741070.21219180.21520250.8880.9071000.19
3.056-3.2660.3141070.22117860.22618930.8540.9011000.203
3.266-3.5280.218780.20716990.20717770.9090.9181000.192
3.528-3.8640.244730.19915550.20116280.9280.9381000.188
3.864-4.3180.225690.19514170.19614870.9390.94599.93270.182
4.318-4.9840.278680.20412530.20713240.9060.94399.77340.196
4.984-6.0990.269460.23810710.23911170.9080.9241000.224
6.099-8.6010.297370.2388520.248890.8990.9321000.227
8.601-82.2690.223290.2174860.2175160.9440.93399.80620.226
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)
10.6494-0.12760.13690.6489-0.25161.35330.03710.1049-0.0224-0.0404-0.0608-0.04770.06820.08980.02370.00920.00650.00360.0257-0.00170.006121.19198.739121.3294
20.6482-0.165-0.15180.66380.11241.46680.04610.09050.0281-0.0415-0.03730.0175-0.0656-0.0755-0.00880.0110.00420.00260.02020.00180.0028-11.3162-8.832821.3429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLB1 - 262
2X-RAY DIFFRACTION2ALLA1 - 262

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