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- PDB-7fjl: Crystal Structure of phthalate dioxygenase from Comamonas testost... -

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Basic information

Entry
Database: PDB / ID: 7fjl
TitleCrystal Structure of phthalate dioxygenase from Comamonas testosteroni KF1
ComponentsRieske (2Fe-2S) domain protein
KeywordsOXIDOREDUCTASE / dioxygenase / bacterial protein / metalloprotein / Rieske domain
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding
Similarity search - Function
LigXa-like, C-terminal domain / LigXa C-terminal domain like / : / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich ...LigXa-like, C-terminal domain / LigXa C-terminal domain like / : / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / 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 / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / S,R MESO-TARTARIC ACID / L(+)-TARTARIC ACID / Rieske (2Fe-2S) domain protein
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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.Biol.Chem. / Year: 2021
Title: Molecular insights into substrate recognition and catalysis by phthalate dioxygenase from Comamonas testosteroni.
Authors: Mahto, J.K. / Neetu, N. / Waghmode, B. / Kuatsjah, E. / Sharma, M. / Sircar, D. / Sharma, A.K. / Tomar, S. / Eltis, L.D. / Kumar, P.
History
DepositionAug 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 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: Rieske (2Fe-2S) domain protein
C: Rieske (2Fe-2S) domain protein
D: Rieske (2Fe-2S) domain protein
E: Rieske (2Fe-2S) domain protein
F: Rieske (2Fe-2S) domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,29440
Polymers295,0106
Non-polymers3,28434
Water47,3432628
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27610 Å2
ΔGint-226 kcal/mol
Surface area89030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.248, 121.375, 161.533
Angle α, β, γ (deg.)90.000, 100.950, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 49168.383 Da / Num. of mol.: 6
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_PD2022 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7WQT1

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Non-polymers , 6 types, 2662 molecules

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


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical
ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2628 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, magnesium chloride, calcium chloride, sodium potassium tartrate

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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 17, 2020 / Details: VERTICAL CRL
RadiationMonochromator: C(110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 2.11→158.59 Å / Num. obs: 191985 / % possible obs: 99 % / Redundancy: 1.8 % / CC1/2: 0.968 / Net I/σ(I): 3.9
Reflection shellResolution: 2.11→2.15 Å / Num. unique obs: 9011 / CC1/2: 0.828 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FHR

7fhr


Resolution: 2.11→158.59 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.87 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 9468 4.9 %RANDOM
Rwork0.166 ---
obs0.1686 182379 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.94 Å2 / Biso mean: 37.679 Å2 / Biso min: 14.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.03 Å2
2---0.15 Å2-0 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.11→158.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19344 0 154 2630 22128
Biso mean--44.11 47.69 -
Num. residues----2459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01220049
X-RAY DIFFRACTIONr_angle_refined_deg2.0461.64627265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8152459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22621.3071132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.683153112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.14215171
X-RAY DIFFRACTIONr_chiral_restr0.1370.22545
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215679
LS refinement shellResolution: 2.11→2.164 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.284 664 -
Rwork0.259 13012 -
obs--95.47 %
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)
10.12790.04660.01320.1101-0.05080.22880.0020.01580.02660.034-0.0377-0.0243-0.02720.02980.03570.0213-0.0249-0.01240.03410.02590.0429-26.32830.132142.2941
20.09420.0636-0.03090.26130.08080.18910.0567-0.0417-0.04590.0483-0.0428-0.03040.00770.0027-0.01390.0437-0.0392-0.03740.05220.03370.0334-37.6832-37.110968.5998
30.0980.00840.00650.2974-0.14770.26190.05770.0195-0.0458-0.0623-0.01370.02510.0318-0.0189-0.0440.04930.0233-0.03610.0508-0.02830.0397-66.21-37.48811.4296
40.0992-0.009-0.02030.17490.04490.2660.0220.02130.02490.0045-0.01690.0154-0.0331-0.0371-0.00510.01950.0230.00790.03150.00210.0474-67.35724.711732.0703
50.09420.0490.07010.1455-0.07370.34950.04950.0519-0.0388-0.0057-0.0348-0.02240.05470.0645-0.01470.03210.0437-0.01750.0679-0.02280.0545-25.5202-42.810523.6281
60.10560.04740.07960.40740.02080.10650.0415-0.0748-0.02330.02170.00720.04030.0104-0.0658-0.04870.0238-0.02960.00270.07860.0350.0367-78.5027-33.867556.4181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 428
2X-RAY DIFFRACTION2B1 - 428
3X-RAY DIFFRACTION3C1 - 423
4X-RAY DIFFRACTION4D1 - 428
5X-RAY DIFFRACTION5E1 - 423
6X-RAY DIFFRACTION6F1 - 425

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