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- PDB-7fhr: Crystal Structure of a Rieske Oxygenase from Cupriavidus metallidurans -

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Basic information

Entry
Database: PDB / ID: 7fhr
TitleCrystal Structure of a Rieske Oxygenase from Cupriavidus metallidurans
ComponentsPutative Phthalate 4,5-dioxygenase, subunit alpha
KeywordsOXIDOREDUCTASE / dioxygenase / bacterial protein / metalloprotein / Rieske domain
Function / homology
Function and homology information


phthalate 4,5-dioxygenase / phthalate 4,5-dioxygenase activity / catabolic process / 2 iron, 2 sulfur cluster binding / 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. / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / GLUTAMIC ACID / GLYCINE / Phthalate 4,5-dioxygenase, subunit alpha
Similarity search - Component
Biological speciesCupriavidus metallidurans CH34 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å
AuthorsMahto, J.K. / Dhankhar, P. / 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
DepositionJul 30, 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 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Phthalate 4,5-dioxygenase, subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,55010
Polymers49,7561
Non-polymers7949
Water6,125340
1
A: Putative Phthalate 4,5-dioxygenase, subunit alpha
hetero molecules

A: Putative Phthalate 4,5-dioxygenase, subunit alpha
hetero molecules

A: Putative Phthalate 4,5-dioxygenase, subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,65130
Polymers149,2683
Non-polymers2,38327
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area12370 Å2
ΔGint-71 kcal/mol
Surface area48820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.416, 103.416, 77.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative Phthalate 4,5-dioxygenase, subunit alpha


Mass: 49756.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans CH34 (bacteria)
Strain: CH34 / Gene: Rmet_5548
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q1LBR9, phthalate 4,5-dioxygenase

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Non-polymers , 7 types, 349 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: glycine, lysine, glutamate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.7377 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2017
RadiationMonochromator: Fe / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7377 Å / Relative weight: 1
ReflectionResolution: 1.84→77.59 Å / Num. obs: 40987 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.999 / Net I/σ(I): 16.3
Reflection shellResolution: 1.84→1.88 Å / Num. unique obs: 2488 / CC1/2: 0.619

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84→58.71 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 8.038 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 2026 4.9 %RANDOM
Rwork0.1644 ---
obs0.1668 38951 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 141.58 Å2 / Biso mean: 43.974 Å2 / Biso min: 25.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å2-0 Å2
3----2.57 Å2
Refinement stepCycle: final / Resolution: 1.84→58.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 42 340 3855
Biso mean--61.11 49.72 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0123628
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.6474910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2655439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89521.524210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08915586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8081530
X-RAY DIFFRACTIONr_chiral_restr0.1160.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022858
LS refinement shellResolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 172 -
Rwork0.336 2825 -
all-2997 -
obs--99.4 %
Refinement TLS params.Method: refined / Origin x: -27.129 Å / Origin y: -17.396 Å / Origin z: -0.303 Å
111213212223313233
T0.0899 Å2-0.0614 Å20.0314 Å2-0.1354 Å2-0.0224 Å2--0.0116 Å2
L0.3992 °2-0.0702 °2-0.0164 °2-0.399 °2-0.0616 °2--0.1321 °2
S-0.0523 Å °-0.0088 Å °-0.0124 Å °-0.0734 Å °0.0771 Å °-0.0158 Å °-0.0549 Å °0.1003 Å °-0.0248 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 439
2X-RAY DIFFRACTION1A501 - 503

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