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- PDB-7q04: Crystal structure of TPADO in a substrate-free state -

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Basic information

Entry
Database: PDB / ID: 7q04
TitleCrystal structure of TPADO in a substrate-free state
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
: / 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: 2.281 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 1.0Apr 6, 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)211,16311
Polymers210,5807
Non-polymers5834
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23310 Å2
ΔGint-179 kcal/mol
Surface area63010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.807, 220.807, 84.093
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:
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
221METMETLEULEUBB1 - 1541 - 154
332METMETLEULEUAA1 - 1541 - 154
442METMETLEULEUCC1 - 1541 - 154
553METMETLEULEUBB1 - 1541 - 154
663METMETLEULEUCC1 - 1541 - 154
774SERSERGLUGLUDD4 - 4106 - 412
884SERSERGLUGLUEE4 - 4106 - 412
995SERSERGLUGLUDD4 - 4106 - 412
10105SERSERGLUGLUFF4 - 4106 - 412
11116GLUGLUMETMETEE3 - 4115 - 413
12126GLUGLUMETMETFF3 - 4115 - 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 , 3 types, 412 molecules

#4: 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
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
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: 0.9762 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: 2.281→110.404 Å / Num. obs: 68994 / % possible obs: 94.3 % / Redundancy: 21.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.053 / Net I/σ(I): 11
Reflection shellResolution: 2.281→2.441 Å / Rmerge(I) obs: 2.767 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3449 / CC1/2: 0.648 / Rpim(I) all: 0.605 / % possible all: 63.3

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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: 2.281→191.224 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.168 / SU B: 15.312 / SU ML: 0.181 / Average fsc free: 0.9049 / Average fsc work: 0.9227 / Cross valid method: FREE R-VALUE / ESU R: 0.591 / ESU R Free: 0.279
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2249 3391 4.916 %
Rwork0.1788 65584 -
all0.181 --
obs-68975 64.739 %
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: 48.369 Å2
Baniso -1Baniso -2Baniso -3
1-0.224 Å20.112 Å20 Å2
2--0.224 Å2-0 Å2
3----0.727 Å2
Refinement stepCycle: LAST / Resolution: 2.281→191.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13651 0 13 408 14072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01313970
X-RAY DIFFRACTIONr_bond_other_d0.0010.01512882
X-RAY DIFFRACTIONr_angle_refined_deg1.7121.63918880
X-RAY DIFFRACTIONr_angle_other_deg1.3121.5829573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80551730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55221.985801
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.376152309
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.014156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.38415106
X-RAY DIFFRACTIONr_chiral_restr0.0730.21785
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023418
X-RAY DIFFRACTIONr_nbd_refined0.1990.22566
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.212182
X-RAY DIFFRACTIONr_nbtor_refined0.1650.26650
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.27006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2478
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0770.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.220
X-RAY DIFFRACTIONr_nbd_other0.2020.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.29
X-RAY DIFFRACTIONr_mcbond_it2.7854.2416953
X-RAY DIFFRACTIONr_mcbond_other2.7844.2416952
X-RAY DIFFRACTIONr_mcangle_it4.3656.3448669
X-RAY DIFFRACTIONr_mcangle_other4.3666.3458670
X-RAY DIFFRACTIONr_scbond_it2.9234.5197017
X-RAY DIFFRACTIONr_scbond_other2.9214.5197017
X-RAY DIFFRACTIONr_scangle_it4.6926.64710204
X-RAY DIFFRACTIONr_scangle_other4.696.64710204
X-RAY DIFFRACTIONr_lrange_it6.5347.82815119
X-RAY DIFFRACTIONr_lrange_other6.53247.81515079
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.054725
X-RAY DIFFRACTIONr_ncsr_local_group_20.1030.054719
X-RAY DIFFRACTIONr_ncsr_local_group_30.090.054786
X-RAY DIFFRACTIONr_ncsr_local_group_40.0920.0511679
X-RAY DIFFRACTIONr_ncsr_local_group_50.0810.0511736
X-RAY DIFFRACTIONr_ncsr_local_group_60.0920.0511729
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.095160.05009
12BX-RAY DIFFRACTIONLocal ncs0.095160.05009
23AX-RAY DIFFRACTIONLocal ncs0.102620.05009
24CX-RAY DIFFRACTIONLocal ncs0.102620.05009
35BX-RAY DIFFRACTIONLocal ncs0.089770.05009
36CX-RAY DIFFRACTIONLocal ncs0.089770.05009
47DX-RAY DIFFRACTIONLocal ncs0.09240.05009
48EX-RAY DIFFRACTIONLocal ncs0.09240.05009
59DX-RAY DIFFRACTIONLocal ncs0.080960.05009
510FX-RAY DIFFRACTIONLocal ncs0.080960.05009
611EX-RAY DIFFRACTIONLocal ncs0.091940.05009
612FX-RAY DIFFRACTIONLocal ncs0.091940.05009
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
2.281-2.3410.267140.2613020.26178420.8670.8344.02960.253
2.341-2.4050.335740.28617810.28876460.7990.82324.26110.275
2.405-2.4740.2891140.26824010.26974340.8590.86333.8310.25
2.474-2.5510.2851340.2628390.26172080.8420.86741.24580.239
2.551-2.6340.2841660.24431190.24669930.8570.87546.97550.221
2.634-2.7270.3062170.24135470.24567810.8550.88355.5080.211
2.727-2.830.2832680.22239370.22565280.8630.89764.41480.192
2.83-2.9450.2812260.22140640.22463050.8830.90468.04120.188
2.945-3.0760.2662050.21942320.22160370.8850.90373.49680.189
3.076-3.2260.2782450.20543710.20857880.8920.91979.75120.179
3.226-3.4010.2322580.244330.20254830.9270.92985.55540.178
3.401-3.6070.2462270.19445900.19752110.9140.93792.43910.175
3.607-3.8560.2262320.18246220.18448990.930.94499.08140.165
3.856-4.1640.2072230.1643520.16245750.9460.9591000.15
4.164-4.5620.1751710.13440170.13641890.9640.9799.97610.129
4.562-5.10.1461770.12536530.12638300.9740.9771000.125
5.1-5.8880.2021340.14432530.14633870.9580.971000.142
5.888-7.210.2151380.15727230.1628610.9480.9591000.159
7.21-10.1890.1871120.14121350.14322470.9560.9671000.155
10.189-191.2240.272560.25912130.25912780.9130.91899.29580.333
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)
10.2425-0.0419-0.11140.7422-0.32390.2155-0.023-0.00330.01420.0432-0.0278-0.0904-0.00550.00340.05070.0845-0.0191-0.03070.0353-0.0370.088281.0786-41.599111.5547
20.66130.01730.04410.1982-0.29360.4425-0.03420.0798-0.02230.01540.0102-0.0175-0.02830.0020.0240.0604-0.0305-0.0140.0426-0.03810.088179.8362-64.0286-5.4082
30.50830.23770.08030.1611-0.15740.9237-0.01750.04320.01760.00120.02980.0222-0.1030.0536-0.01230.0638-0.0278-0.01230.0528-0.02360.083859.2616-44.767-6.2058
40.1368-0.03880.24520.6952-0.0850.4741-0.0736-0.06250.01470.1630.0605-0.0386-0.0987-0.07350.01310.1260.06270.01340.0894-0.04970.067661.6029-44.732435.6695
50.1656-0.14250.07650.2043-0.05840.1481-0.0018-0.008-0.06330.02250.0238-0.00180.0037-0.0099-0.02210.0595-0.0212-0.02030.0239-0.01610.091176.5608-83.7718.7345
60.2643-0.02460.18240.20080.03880.1648-0.0092-0.0387-0.0616-0.01590.01030.1392-0.0077-0.0562-0.0010.0077-0.01370.00620.0641-0.01740.145638.9494-66.1814.2983
70.56660.1252-0.38080.1578-0.00262.2890.07020.14090.17250.0505-0.0550.0740.0063-0.1641-0.01530.04240.0007-0.01270.08670.01230.159174.4872-16.6509-16.6664
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 DIFFRACTION4ALLD4 - 410
5X-RAY DIFFRACTION4ALLD501
6X-RAY DIFFRACTION5ALLE3 - 420
7X-RAY DIFFRACTION6ALLF3 - 411
8X-RAY DIFFRACTION7ALLH1 - 129

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