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- PDB-6qga: Crystal structure of Ideonella sakaiensis MHETase bound to the no... -

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Entry
Database: PDB / ID: 6qga
TitleCrystal structure of Ideonella sakaiensis MHETase bound to the non-hydrolyzable ligand MHETA
ComponentsMono(2-hydroxyethyl) terephthalate hydrolase
KeywordsHYDROLASE / Plastic-degrading hydrolase / alpha/beta hydrolase fold / I. sakaiensis catalytic triad
Function / homology
Function and homology information


mono(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / cell outer membrane / metal ion binding
Similarity search - Function
Tannase/feruloyl esterase / Tannase and feruloyl esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
4-(2-hydroxyethylcarbamoyl)benzoic acid / Mono(2-hydroxyethyl) terephthalate hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPalm, G.J. / Reisky, L. / Boettcher, D. / Mueller, H. / Michels, E.A.P. / Walczak, C. / Berndt, L. / Weiss, M.S. / Bornscheuer, U.T. / Weber, G.
CitationJournal: Nat Commun / Year: 2019
Title: Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate.
Authors: Palm, G.J. / Reisky, L. / Bottcher, D. / Muller, H. / Michels, E.A.P. / Walczak, M.C. / Berndt, L. / Weiss, M.S. / Bornscheuer, U.T. / Weber, G.
History
DepositionJan 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _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
Revision 1.4Nov 13, 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: Mono(2-hydroxyethyl) terephthalate hydrolase
B: Mono(2-hydroxyethyl) terephthalate hydrolase
C: Mono(2-hydroxyethyl) terephthalate hydrolase
D: Mono(2-hydroxyethyl) terephthalate hydrolase
E: Mono(2-hydroxyethyl) terephthalate hydrolase
F: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,73638
Polymers377,0656
Non-polymers3,67132
Water47,5602640
1
A: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5007
Polymers62,8441
Non-polymers6566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5358
Polymers62,8441
Non-polymers6917
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3746
Polymers62,8441
Non-polymers5295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0933
Polymers62,8441
Non-polymers2492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6437
Polymers62,8441
Non-polymers7996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5917
Polymers62,8441
Non-polymers7476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.153, 183.646, 246.752
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, 6 molecules ABCDEF

#1: Protein
Mono(2-hydroxyethyl) terephthalate hydrolase / MHETase


Mass: 62844.129 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_0224
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0K8P8E7, mono(ethylene terephthalate) hydrolase

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Non-polymers , 6 types, 2672 molecules

#2: Chemical
ChemComp-J1K / 4-(2-hydroxyethylcarbamoyl)benzoic acid


Mass: 209.199 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H11NO4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2640 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 30% (v/v) 2,4-MPD and 0.12 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 293388 / % possible obs: 98.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.993 / Rrim(I) all: 0.212 / Rsym value: 0.195 / Net I/σ(I): 8.85
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.054 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 44417 / CC1/2: 0.602 / Rrim(I) all: 1.18 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G21

6g21


Resolution: 2.1→49.107 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.37
RfactorNum. reflection% reflection
Rfree0.198 3081 1.05 %
Rwork0.1731 --
obs0.1733 293303 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24746 0 226 2640 27612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125645
X-RAY DIFFRACTIONf_angle_d1.0434933
X-RAY DIFFRACTIONf_dihedral_angle_d13.56115024
X-RAY DIFFRACTIONf_chiral_restr0.0623645
X-RAY DIFFRACTIONf_plane_restr0.0084665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0974-2.13020.35471180.30811138X-RAY DIFFRACTION84
2.1302-2.16510.32971320.282412395X-RAY DIFFRACTION94
2.1651-2.20240.2711380.270113065X-RAY DIFFRACTION99
2.2024-2.24250.25781410.249313255X-RAY DIFFRACTION100
2.2425-2.28560.26271400.231713186X-RAY DIFFRACTION100
2.2856-2.33230.25671410.231913238X-RAY DIFFRACTION100
2.3323-2.3830.26151400.227713233X-RAY DIFFRACTION100
2.383-2.43840.27491410.219813283X-RAY DIFFRACTION100
2.4384-2.49940.22781410.217213239X-RAY DIFFRACTION100
2.4994-2.56690.24041400.215513216X-RAY DIFFRACTION100
2.5669-2.64250.22971410.21213245X-RAY DIFFRACTION100
2.6425-2.72780.24161410.202113346X-RAY DIFFRACTION100
2.7278-2.82520.20661410.178313289X-RAY DIFFRACTION100
2.8252-2.93830.20581410.172113286X-RAY DIFFRACTION100
2.9383-3.07210.17791420.163813336X-RAY DIFFRACTION100
3.0721-3.2340.18361410.1613325X-RAY DIFFRACTION100
3.234-3.43660.16541420.15213345X-RAY DIFFRACTION100
3.4366-3.70180.19261420.137413415X-RAY DIFFRACTION100
3.7018-4.07420.14731420.129213415X-RAY DIFFRACTION100
4.0742-4.66330.15441440.119113484X-RAY DIFFRACTION100
4.6633-5.87380.14221440.14513570X-RAY DIFFRACTION100
5.8738-49.12080.18251480.158513918X-RAY DIFFRACTION99
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)
11.88120.91510.30841.1391-0.06980.722-0.04810.02540.2079-0.0368-0.03530.2365-0.1882-0.12620.06670.29140.0591-0.04470.2767-0.03510.31175.27121.3063-64.7117
21.47250.22610.44580.69880.0140.77190.1237-0.4368-0.20630.2224-0.1128-0.00530.0752-0.2213-0.01380.3031-0.0386-0.01980.37730.04880.324211.2567-19.6148-45.3504
30.6061-0.16831.1080.6814-0.07052.05550.0238-0.1022-0.05610.0744-0.0392-0.1207-0.0290.1111-0.00490.266-0.0073-0.02640.30940.03960.350430.5448-11.1397-50.3382
41.6185-0.1840.76220.28710.031.3751-0.0218-0.2094-0.07090.1260.0190.06680.0641-0.17050.01870.2594-0.00750.02320.25290.020.2603-26.712-25.858119.5382
50.74610.06240.30340.50.19470.82820.0490.0948-0.11780.0118-0.0004-0.0310.12910.0671-0.04820.23730.002-0.00360.2361-0.00440.2614-16.846-33.9887-5.7761
62.1213-0.2841-0.91970.5252-0.08931.2782-0.0237-0.20490.05010.1440.0292-0.061-0.13090.1217-0.0050.3006-0-0.01190.2385-0.02060.2741-23.55026.951819.1949
71.10310.077-0.24510.8365-0.31730.8320.01720.22470.1719-0.09240.0031-0.0277-0.1942-0.0633-0.0120.32490.01060.02490.27550.01950.2724-28.891114.8317-7.941
81.7261-1.05880.44613.3618-0.86132.2450.06790.20640.0862-0.1153-0.02160.2644-0.2652-0.3083-0.0660.27320.05580.02670.34470.01680.2971-48.608814.08670.8809
92.30.9367-0.0630.9740.23260.84-0.06450.0496-0.1887-0.03580.0369-0.19410.1690.17080.00440.29210.05370.0190.28080.03020.295646.518413.0971-65.0964
101.02690.0077-0.40330.52210.08180.85370.0035-0.26590.03130.1709-0.0048-0.0565-0.00540.28250.00110.2964-0.0016-0.03980.32640.01190.263541.551731.3599-42.9828
110.97850.0001-1.51321.2871-0.40453.3168-0.0129-0.0232-0.03640.1488-0.01440.17390.0873-0.13260.02090.2574-0.0113-0.01760.24850.00370.285921.915823.7307-48.0563
121.8218-0.41750.75320.7846-0.18070.7191-0.05350.11090.1177-0.10270.0339-0.0544-0.07910.06660.02860.2594-0.02930.02550.2495-0.00920.21214.3437-31.730631.3361
130.79570.01560.11220.6621-0.00890.303-0.0243-0.0281-0.1351-0.05110.03480.04160.083-0.0468-0.00930.2652-0.02530.00320.26210.01850.22664.3745-58.362137.9201
141.1125-0.156-0.07821.0620.16960.4572-0.0516-0.0462-0.1621-0.01720.0667-0.0460.1156-0.014-0.01250.2671-0.0130.01020.2640.02430.238110.1902-59.186341.0387
151.47950.7530.11513.37711.77682.3015-0.07480.0298-0.074-0.13240.03140.29810.0918-0.2520.06030.2431-0.0216-0.03170.29770.03810.2765-11.0533-50.672933.8303
162.1328-0.65740.82651.2094-0.20520.5655-0.07260.16930.1502-0.16410.0135-0.1395-0.13510.14160.07130.323-0.02990.00190.303-0.00920.27348.5314-13.4537-94.1232
170.96110.08410.08961.05880.22410.5325-0.08450.047-0.1359-0.08690.0879-0.07870.06840.0464-0.00660.28710.01060.01180.2607-0.00710.25950.859-39.836-89.1605
183.695-0.83622.1721.78052.00316.2524-0.0189-0.1483-0.1987-0.1528-0.02280.29910.0829-0.93070.02850.2996-0.0441-0.01640.27090.04480.3403-20.9523-37.4646-94.0912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 212 )
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 523 )
3X-RAY DIFFRACTION3chain 'A' and (resid 524 through 602 )
4X-RAY DIFFRACTION4chain 'B' and (resid 43 through 212 )
5X-RAY DIFFRACTION5chain 'B' and (resid 213 through 603 )
6X-RAY DIFFRACTION6chain 'C' and (resid 43 through 212 )
7X-RAY DIFFRACTION7chain 'C' and (resid 213 through 523 )
8X-RAY DIFFRACTION8chain 'C' and (resid 524 through 603 )
9X-RAY DIFFRACTION9chain 'D' and (resid 43 through 212 )
10X-RAY DIFFRACTION10chain 'D' and (resid 213 through 523 )
11X-RAY DIFFRACTION11chain 'D' and (resid 524 through 603 )
12X-RAY DIFFRACTION12chain 'E' and (resid 43 through 212 )
13X-RAY DIFFRACTION13chain 'E' and (resid 213 through 333 )
14X-RAY DIFFRACTION14chain 'E' and (resid 334 through 523 )
15X-RAY DIFFRACTION15chain 'E' and (resid 524 through 603 )
16X-RAY DIFFRACTION16chain 'F' and (resid 43 through 212 )
17X-RAY DIFFRACTION17chain 'F' and (resid 213 through 560 )
18X-RAY DIFFRACTION18chain 'F' and (resid 561 through 603 )

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