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- PDB-7q06: Crystal structure of TPADO in complex with 2-OH-TPA -

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Basic information

Entry
Database: PDB / ID: 7q06
TitleCrystal structure of TPADO in complex with 2-OH-TPA
Components
  • (Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit ...) x 2
  • Lysozyme
KeywordsOXIDOREDUCTASE / terephthalic acid / TPA
Function / homology
Function and homology information


terephthalate 1,2-dioxygenase / terephthalate 1,2-dioxygenase activity / phthalate metabolic process / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / 2 iron, 2 sulfur cluster binding / cell wall macromolecule catabolic process / lysozyme ...terephthalate 1,2-dioxygenase / terephthalate 1,2-dioxygenase activity / phthalate metabolic process / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / 2 iron, 2 sulfur cluster binding / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / iron ion binding / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Ring-hydroxylating dioxygenase, large/alpha subunit AhdA1c-like, C-terminal / SnoaL-like domain / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / SnoaL-like domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain ...Ring-hydroxylating dioxygenase, large/alpha subunit AhdA1c-like, C-terminal / SnoaL-like domain / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / SnoaL-like domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme-like domain superfamily
Similarity search - Domain/homology
2-Hydroxyterephthalic acid / : / FE2/S2 (INORGANIC) CLUSTER / Lysozyme C / Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 / Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1
Similarity search - Component
Biological speciesComamonas sp. (bacteria)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZahn, M. / Kincannon, W.M. / DuBois, J.L. / McGeehan, J.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Biochemical and structural characterization of an aromatic ring-hydroxylating dioxygenase for terephthalic acid catabolism.
Authors: Kincannon, W.M. / Zahn, M. / Clare, R. / Lusty Beech, J. / Romberg, A. / Larson, J. / Bothner, B. / Beckham, G.T. / McGeehan, J.E. / DuBois, J.L.
History
DepositionOct 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 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
A: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1
B: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1
C: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1
D: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2
E: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2
F: Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2
H: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,34221
Polymers210,5807
Non-polymers1,76214
Water16,592921
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25630 Å2
ΔGint-310 kcal/mol
Surface area62160 Å2
Unit cell
Length a, b, c (Å)220.312, 220.312, 83.175
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53B
63C
74D
84E
95D
105F
116E
126F

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETLEULEUAA1 - 1541 - 154
211METMETLEULEUBB1 - 1541 - 154
322METMETLEULEUAA1 - 1541 - 154
422METMETLEULEUCC1 - 1541 - 154
533METMETLEULEUBB1 - 1541 - 154
633METMETLEULEUCC1 - 1541 - 154
744GLUGLUGLUGLUDD3 - 4105 - 412
844GLUGLUGLUGLUEE3 - 4105 - 412
955SERSERMETMETDD4 - 4116 - 413
1055SERSERMETMETFF4 - 4116 - 413
1166SERSERMETMETEE4 - 4116 - 413
1266SERSERMETMETFF4 - 4116 - 413

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

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Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit ... , 2 types, 6 molecules ABCDEF

#1: Protein Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit beta 1 / TPADO terminal oxygenase component / TER dioxygenase system / TERDOS / Terephthalate 1 / 2- ...TPADO terminal oxygenase component / TER dioxygenase system / TERDOS / Terephthalate 1 / 2-dioxygenase small subunit 1


Mass: 17249.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas sp. (bacteria) / Gene: tphA3I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3C1E2, terephthalate 1,2-dioxygenase
#2: Protein Terephthalate 1,2-dioxygenase, terminal oxygenase component subunit alpha 2 / TPADO terminal oxygenase component / TER dioxygenase system / TERDOS / Terephthalate 1 / 2- ...TPADO terminal oxygenase component / TER dioxygenase system / TERDOS / Terephthalate 1 / 2-dioxygenase large subunit 2


Mass: 48166.754 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas sp. (bacteria) / Gene: tphA2II / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3C1D5, terephthalate 1,2-dioxygenase

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Protein , 1 types, 1 molecules H

#3: Protein Lysozyme


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme

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Non-polymers , 5 types, 935 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-8IB / 2-Hydroxyterephthalic acid / 2-oxidanylterephthalic acid / 2-hydroxybenzene-1,4-dicarboxylic acid / 2-hydroxyterephthalate


Mass: 182.130 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H6O5 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12.5% MPD, 12.5% PEG 3350, 12.5% PEG 1000, 0.3 M sodium nitrate, 0.3 M sodium phosphate dibasic, 0.3 M ammonium sulfate, 0.1 M buffer Imidazole/MES 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: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.948→190.796 Å / Num. obs: 149913 / % possible obs: 96.4 % / Redundancy: 17.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.027 / Net I/σ(I): 17.9
Reflection shellResolution: 1.948→2.057 Å / Redundancy: 18.5 % / Rmerge(I) obs: 2.372 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7497 / CC1/2: 0.59 / Rpim(I) all: 0.56 / % possible all: 57.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N0Q, 3EBY

3n0q

3eby


Resolution: 1.95→190.796 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.361 / SU ML: 0.102 / Cross valid method: FREE R-VALUE / ESU R: 0.144 / ESU R Free: 0.134
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2022 7226 4.82 %
Rwork0.1648 142677 -
all0.167 --
obs-149903 89.47 %
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: 43.123 Å2
Baniso -1Baniso -2Baniso -3
1-0.027 Å20.014 Å20 Å2
2--0.027 Å2-0 Å2
3----0.089 Å2
Refinement stepCycle: LAST / Resolution: 1.95→190.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13861 0 83 921 14865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01314277
X-RAY DIFFRACTIONr_bond_other_d0.0010.01513074
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.63819317
X-RAY DIFFRACTIONr_angle_other_deg1.4491.5830030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.48251764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37422.005818
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.079152348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.99315106
X-RAY DIFFRACTIONr_chiral_restr0.0850.21816
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023499
X-RAY DIFFRACTIONr_nbd_refined0.2010.22599
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.212322
X-RAY DIFFRACTIONr_nbtor_refined0.1690.26842
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.26780
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2888
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.233
X-RAY DIFFRACTIONr_nbd_other0.2430.2116
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.219
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0110.21
X-RAY DIFFRACTIONr_mcbond_it2.8353.6737056
X-RAY DIFFRACTIONr_mcbond_other2.8353.6727055
X-RAY DIFFRACTIONr_mcangle_it3.945.4848802
X-RAY DIFFRACTIONr_mcangle_other3.945.4848803
X-RAY DIFFRACTIONr_scbond_it3.7764.0547221
X-RAY DIFFRACTIONr_scbond_other3.7724.0537217
X-RAY DIFFRACTIONr_scangle_it5.3775.9310503
X-RAY DIFFRACTIONr_scangle_other5.3785.9310502
X-RAY DIFFRACTIONr_lrange_it7.05242.88315878
X-RAY DIFFRACTIONr_lrange_other7.04642.5415660
X-RAY DIFFRACTIONr_ncsr_local_group_10.0980.054729
X-RAY DIFFRACTIONr_ncsr_local_group_20.10.054711
X-RAY DIFFRACTIONr_ncsr_local_group_30.0790.054834
X-RAY DIFFRACTIONr_ncsr_local_group_40.1030.0512030
X-RAY DIFFRACTIONr_ncsr_local_group_50.0870.0512095
X-RAY DIFFRACTIONr_ncsr_local_group_60.0990.0511972
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.098430.05009
12BX-RAY DIFFRACTIONLocal ncs0.098430.05009
23AX-RAY DIFFRACTIONLocal ncs0.099560.05009
24CX-RAY DIFFRACTIONLocal ncs0.099560.05009
35BX-RAY DIFFRACTIONLocal ncs0.078840.05009
36CX-RAY DIFFRACTIONLocal ncs0.078840.05009
47DX-RAY DIFFRACTIONLocal ncs0.103140.05008
48EX-RAY DIFFRACTIONLocal ncs0.103140.05008
59DX-RAY DIFFRACTIONLocal ncs0.087080.05008
510FX-RAY DIFFRACTIONLocal ncs0.087080.05008
611EX-RAY DIFFRACTIONLocal ncs0.099280.05008
612FX-RAY DIFFRACTIONLocal ncs0.099280.05008
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
1.95-2.0010.334570.2639840.267123720.7450.8048.41420.255
2.001-2.0550.2742790.26858980.268119890.8330.81651.52220.26
2.055-2.1150.2615290.248106760.248116510.8650.85696.1720.234
2.115-2.180.2675880.232108300.234114230.8710.88299.95620.213
2.18-2.2520.2345570.208104390.21109960.9080.9131000.184
2.252-2.3310.2395240.185101190.187106430.9150.9321000.159
2.331-2.4190.224820.17797870.179102690.9330.941000.151
2.419-2.5170.2374850.16894280.17199130.9250.9481000.142
2.517-2.6290.2154550.16390330.16594880.940.9541000.14
2.629-2.7580.2054440.15686590.15891030.9470.9571000.135
2.758-2.9070.2123870.1682770.16286640.9460.9581000.141
2.907-3.0830.2393830.17378130.17681960.930.9491000.155
3.083-3.2960.2253740.17473110.17676850.9430.9541000.161
3.296-3.560.2023230.17568590.17671830.9490.96199.98610.167
3.56-3.8990.1992800.16863290.16966090.9560.9631000.164
3.899-4.3590.1693360.13856880.1460240.9680.9741000.139
4.359-5.0330.1492850.11349970.11552820.9770.9811000.121
5.033-6.1640.1832130.1542930.15245060.9660.9731000.157
6.164-8.7120.1891350.15333840.15535190.9650.9721000.164
8.712-190.7960.1971100.18318710.18419860.9660.95799.74820.217
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)
10.2919-0.06060.24390.5862-0.31870.33680.05390.03470.0102-0.0197-0.0837-0.04170.03480.04830.02980.10450.04290.00010.04740.00410.044280.871841.59980.8452
20.4724-0.00660.06160.3697-0.30990.37740.0156-0.07860.02050.0264-0.0309-0.01160.00350.02230.01530.07340.03110.00360.0504-0.00440.059579.651963.734918.0143
30.3827-0.3414-0.00570.4041-0.16430.362-0.0145-0.0349-0.01830.01480.05260.05540.06870.0224-0.03810.09180.036-0.01180.05440.00960.059359.110444.565918.4663
40.133-0.0069-0.13130.17970.0790.36180.01450.07280.0208-0.11610.00250.03770.1007-0.0417-0.0170.19520.0298-0.040.04750.00570.01662.406844.972-23.5876
50.05250.0459-0.00440.2995-0.0280.07660.02730.00340.0552-0.0443-0.0126-0.0063-0.00330.0078-0.01470.0650.03360.03680.04240.01250.084576.146383.9332-6.2624
60.3160.0412-0.1350.13830.00410.13430.02160.01750.0494-0.01460.01080.10080.0151-0.0434-0.03240.04090.0197-0.01840.06090.01980.096838.688965.63248.0501
70.83360.05480.71630.0907-0.13011.83030.0203-0.2219-0.1088-0.0534-0.0331-0.0264-0.0203-0.21180.01280.06480.01270.00760.07680.03380.077674.147816.55929.0008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 154
2X-RAY DIFFRACTION2ALLB1 - 154
3X-RAY DIFFRACTION3ALLC1 - 154
4X-RAY DIFFRACTION4ALLD3 - 411
5X-RAY DIFFRACTION4ALLD501
6X-RAY DIFFRACTION5ALLE3 - 424
7X-RAY DIFFRACTION5ALLE501
8X-RAY DIFFRACTION5ALLE502
9X-RAY DIFFRACTION6ALLF4 - 412
10X-RAY DIFFRACTION6ALLF501
11X-RAY DIFFRACTION7ALLH1 - 129

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