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- PDB-7vju: Crystal Structure of terephthalate dioxygenase from Comamonas tes... -

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Basic information

Entry
Database: PDB / ID: 7vju
TitleCrystal Structure of terephthalate dioxygenase from Comamonas testosteroni KF1
Components
  • Aromatic-ring-hydroxylating dioxygenase beta subunit
  • Rieske (2Fe-2S) domain protein
KeywordsOXIDOREDUCTASE / dioxygenase / bacterial protein / metalloprotein / Rieske domain
Function / homology
Function and homology information


dioxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding
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 Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur 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 Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Aromatic-ring-hydroxylating dioxygenase beta subunit / Rieske (2Fe-2S) domain protein
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsMahto, J.K. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/HRD/NBA/37/01/2015 (VIII) India
CitationJournal: J.Bacteriol. / Year: 2022
Title: Structural Insights into Dihydroxylation of Terephthalate, a Product of Polyethylene Terephthalate Degradation.
Authors: Mahto, J.K. / Neetu, N. / Sharma, M. / Dubey, M. / Vellanki, B.P. / Kumar, P.
History
DepositionSep 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rieske (2Fe-2S) domain protein
B: Aromatic-ring-hydroxylating dioxygenase beta subunit
C: Rieske (2Fe-2S) domain protein
D: Aromatic-ring-hydroxylating dioxygenase beta subunit
E: Rieske (2Fe-2S) domain protein
F: Aromatic-ring-hydroxylating dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,07333
Polymers191,2156
Non-polymers2,85827
Water16,484915
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30060 Å2
ΔGint-256 kcal/mol
Surface area53880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.561, 134.213, 145.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein Rieske (2Fe-2S) domain protein


Mass: 46399.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (strain DSM 14576 / KF-1) (bacteria)
Strain: DSM 14576 / KF-1 / Gene: CtesDRAFT_PD2130 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7WRJ9
#2: Protein Aromatic-ring-hydroxylating dioxygenase beta subunit


Mass: 17338.504 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (strain DSM 14576 / KF-1) (bacteria)
Strain: DSM 14576 / KF-1 / Gene: CtesDRAFT_PD2129 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7WRJ8

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Non-polymers , 7 types, 942 molecules

#3: 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
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.4 M Ammonium phosphate dibasic, 0.1 M Tris pH 8.5, and 4% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.27→67.15 Å / Num. obs: 79803 / % possible obs: 96.7 % / Redundancy: 1.9 % / CC1/2: 0.984 / Net I/σ(I): 16.5
Reflection shellResolution: 2.27→2.32 Å / Num. unique obs: 4634 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gzx

3gzx


Resolution: 2.27→67.15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.588 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 3959 5 %RANDOM
Rwork0.1567 ---
obs0.1598 75843 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 153.8 Å2 / Biso mean: 51.09 Å2 / Biso min: 24.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2---0.02 Å20 Å2
3----1.59 Å2
Refinement stepCycle: final / Resolution: 2.27→67.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12676 0 145 915 13736
Biso mean--66.42 53.56 -
Num. residues----1609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01213087
X-RAY DIFFRACTIONr_angle_refined_deg2.0191.63117677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.12751602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73222.032748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.548152133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4361595
X-RAY DIFFRACTIONr_chiral_restr0.1540.21662
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210032
LS refinement shellResolution: 2.274→2.333 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 287 -
Rwork0.234 5695 -
all-5982 -
obs--99.22 %
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)
10.39740.12930.08710.3883-0.22110.21780.01860.0383-0.0505-0.0685-0.1319-0.11030.03850.11830.11330.12110.04020.00820.23570.0340.195942.2133-11.1369-21.0963
20.57790.2818-0.23560.4481-0.52370.64340.006-0.0797-0.13780.1808-0.0797-0.085-0.2370.03490.07370.2706-0.0116-0.0890.25230.03360.069834.5776-2.59497.7642
30.2309-0.2010.12390.3604-0.16550.2771-0.0209-0.0931-0.0534-0.1110.19120.12770.0522-0.0332-0.17040.1377-0.0199-0.03390.16190.09170.2481-1.5167-14.8042-22.5047
40.31970.06870.46370.26810.08180.7776-0.01-0.1132-0.12390.05870.13830.0344-0.0395-0.0518-0.12820.16280.05460.05920.2930.1490.110310.5433-16.66525.4962
50.2222-0.06310.09330.3248-0.30620.2996-0.08580.06880.07210.12410.049-0.0108-0.1509-0.02210.03680.2455-0.0051-0.03940.1109-0.03970.209617.869225.659-18.0773
60.8232-0.88010.30340.9634-0.32380.1119-0.3079-0.2593-0.05630.29240.32680.0431-0.113-0.0921-0.01890.33860.15660.02380.3128-0.04430.022110.142210.9888.4242
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 607
2X-RAY DIFFRACTION2B2 - 154
3X-RAY DIFFRACTION3C5 - 602
4X-RAY DIFFRACTION4D1 - 201
5X-RAY DIFFRACTION5E5 - 606
6X-RAY DIFFRACTION6F2 - 202

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