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- PDB-7qjq: Crystal structure of a cutinase enzyme from Thermobifida fusca NT... -

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Basic information

Entry
Database: PDB / ID: 7qjq
TitleCrystal structure of a cutinase enzyme from Thermobifida fusca NTU22 (702)
ComponentsAcetylxylan esterase
KeywordsHYDROLASE / plastic degradation
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / periplasmic space / extracellular region
Similarity search - Function
Chlorophyllase / Chlorophyllase / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Cutinase cut2
Similarity search - Component
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsZahn, M. / Gill, R.S. / Avilan, L. / 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylxylan esterase
B: Acetylxylan esterase
C: Acetylxylan esterase
D: Acetylxylan esterase
E: Acetylxylan esterase
F: Acetylxylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,92512
Polymers177,2886
Non-polymers6376
Water27,2931515
1
A: Acetylxylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6542
Polymers29,5481
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetylxylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6542
Polymers29,5481
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acetylxylan esterase


Theoretical massNumber of molelcules
Total (without water)29,5481
Polymers29,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acetylxylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6542
Polymers29,5481
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Acetylxylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7603
Polymers29,5481
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Acetylxylan esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6542
Polymers29,5481
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.346, 79.753, 120.133
Angle α, β, γ (deg.)86.280, 87.940, 89.500
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA2 - 2633 - 264
21LEULEUBB2 - 2633 - 264
12PHEPHEAA2 - 2623 - 263
22PHEPHECC2 - 2623 - 263
13PHEPHEAA2 - 2623 - 263
23PHEPHEDD2 - 2623 - 263
14PHEPHEAA2 - 2623 - 263
24PHEPHEEE2 - 2623 - 263
15PROPROAA2 - 2613 - 262
25PROPROFF2 - 2613 - 262
16LEULEUBB1 - 2632 - 264
26LEULEUCC1 - 2632 - 264
17PROPROBB1 - 2612 - 262
27PROPRODD1 - 2612 - 262
18PROPROBB1 - 2612 - 262
28PROPROEE1 - 2612 - 262
19PHEPHEBB1 - 2622 - 263
29PHEPHEFF1 - 2622 - 263
110PHEPHECC1 - 2622 - 263
210PHEPHEDD1 - 2622 - 263
111PHEPHECC1 - 2622 - 263
211PHEPHEEE1 - 2622 - 263
112PHEPHECC1 - 2622 - 263
212PHEPHEFF1 - 2622 - 263
113PHEPHEDD1 - 2622 - 263
213PHEPHEEE1 - 2622 - 263
114PHEPHEDD1 - 2622 - 263
214PHEPHEFF1 - 2622 - 263
115PHEPHEEE1 - 2622 - 263
215PHEPHEFF1 - 2622 - 263

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Acetylxylan esterase


Mass: 29548.064 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E0Z5H1
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1515 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 20 % PEG 3350, 0.2 M sodium sulfate, 0.1 M Bis-Tris propane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.637→119.804 Å / Num. obs: 140392 / % possible obs: 89.5 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.055 / Net I/σ(I): 9
Reflection shellResolution: 1.637→1.748 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7020 / CC1/2: 0.567 / Rpim(I) all: 0.481 / % possible all: 53.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5zoa

5zoa


Resolution: 1.64→119.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.879 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 6780 4.8 %RANDOM
Rwork0.1652 ---
obs0.1668 133556 76.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.54 Å2 / Biso mean: 20.544 Å2 / Biso min: 1.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0.05 Å20.03 Å2
2--0.06 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 1.64→119.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11924 0 42 1515 13481
Biso mean--49.99 31.69 -
Num. residues----1561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01312383
X-RAY DIFFRACTIONr_bond_other_d0.0010.01411422
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.64516927
X-RAY DIFFRACTIONr_angle_other_deg1.4831.5726365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76251598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1921.087607
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.925151859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8741591
X-RAY DIFFRACTIONr_chiral_restr0.090.21680
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214149
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022873
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A88360.07
12B88360.07
21A89030.06
22C89030.06
31A88330.07
32D88330.07
41A88550.06
42E88550.06
51A87770.07
52F87770.07
61B87570.07
62C87570.07
71B89600.04
72D89600.04
81B89210.05
82E89210.05
91B87550.07
92F87550.07
101C87760.08
102D87760.08
111C87740.08
112E87740.08
121C87630.07
122F87630.07
131D90060.06
132E90060.06
141D87640.07
142F87640.07
151E88260.06
152F88260.06
LS refinement shellResolution: 1.64→1.683 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 81 -
Rwork0.26 1424 -
all-1505 -
obs--11 %
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)
10.1647-0.1304-0.04190.3188-0.04650.40880.0323-0.0417-0.0188-0.043-0.01980.02570.00380.0482-0.01250.0117-0.0008-0.00770.0266-0.00390.03820.0846-0.2966-0.2708
20.11260.0031-0.01470.46640.00780.3210.02170.00870.01710.0246-0.0374-0.0043-0.0153-0.01490.01570.01660.0010.00630.0046-0.00270.0509-12.270337.360210.549
30.1240.2084-0.01850.40750.12890.53830.02730.01850.01130.04620.0084-0.00430.0269-0.0514-0.03570.01270.00890.00280.01840.01140.046-28.331539.5255-26.9003
40.0513-0.0449-0.13490.4523-0.08430.75560.01620.0212-0.01840.0181-0.05850.0397-0.06140.03660.04230.00860.0017-0.00830.0317-0.00340.0268-16.0716-2.6828-37.7414
50.2640.02950.18040.2941-0.19890.50140.0461-0.0219-0.0351-0.0427-0.01220.00820.0287-0.0144-0.03390.02560.0061-0.0140.0207-0.00530.03-43.335548.2072-64.5142
60.67090.00090.91640.10630.08571.31910.1443-0.1393-0.0644-0.0431-0.0126-0.07150.1449-0.2077-0.13170.0471-0.02710.01370.06210.03780.0564-28.639380.0254-83.0245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 301
2X-RAY DIFFRACTION2B1 - 301
3X-RAY DIFFRACTION3C1 - 301
4X-RAY DIFFRACTION4D1 - 301
5X-RAY DIFFRACTION5E1 - 301
6X-RAY DIFFRACTION6F1 - 301

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