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- PDB-9jp5: Phthalate 3,4-dioxygenase from Rhodococcus jostii RHA1 -

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Basic information

Entry
Database: PDB / ID: 9jp5
TitlePhthalate 3,4-dioxygenase from Rhodococcus jostii RHA1
Components
  • Phthalate 3,4-dioxygenase alpha subunit
  • Phthalate 3,4-dioxygenase beta subunit
KeywordsOXIDOREDUCTASE / 2Fe-2S binding / iron binding / Dioxygenase activity / Aromatic hydrocarbons catabolism
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor / dioxygenase activity / catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / 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. / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain ...Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / 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. / 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
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / Phthalate 3,4-dioxygenase alpha subunit / Phthalate 3,4-dioxygenase beta subunit
Similarity search - Component
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsKumar, K.A. / Kumar, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT-2771-BIO-CNA India
CitationJournal: To Be Published
Title: phthalate 3,4-dioxygenase from Rhodococcus jostii RHA1
Authors: Kumar, K.A.
History
DepositionSep 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phthalate 3,4-dioxygenase alpha subunit
B: Phthalate 3,4-dioxygenase beta subunit
C: Phthalate 3,4-dioxygenase alpha subunit
D: Phthalate 3,4-dioxygenase beta subunit
E: Phthalate 3,4-dioxygenase alpha subunit
F: Phthalate 3,4-dioxygenase beta subunit
G: Phthalate 3,4-dioxygenase alpha subunit
H: Phthalate 3,4-dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,26016
Polymers324,3338
Non-polymers9278
Water9,458525
1
A: Phthalate 3,4-dioxygenase alpha subunit
B: Phthalate 3,4-dioxygenase beta subunit
C: Phthalate 3,4-dioxygenase alpha subunit
D: Phthalate 3,4-dioxygenase beta subunit
E: Phthalate 3,4-dioxygenase alpha subunit
F: Phthalate 3,4-dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,94512
Polymers243,2506
Non-polymers6956
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32070 Å2
ΔGint-206 kcal/mol
Surface area59710 Å2
MethodPISA
2
G: Phthalate 3,4-dioxygenase alpha subunit
H: Phthalate 3,4-dioxygenase beta subunit
hetero molecules

G: Phthalate 3,4-dioxygenase alpha subunit
H: Phthalate 3,4-dioxygenase beta subunit
hetero molecules

G: Phthalate 3,4-dioxygenase alpha subunit
H: Phthalate 3,4-dioxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,94512
Polymers243,2506
Non-polymers6956
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area32010 Å2
ΔGint-211 kcal/mol
Surface area59860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.599, 194.599, 157.287
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Phthalate 3,4-dioxygenase alpha subunit


Mass: 57149.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Gene: padAa, RHA1_ro08167, RHA1_ro10208 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q0RWD5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor
#2: Protein
Phthalate 3,4-dioxygenase beta subunit / Terminal oxygenase small subunit of phthalate dioxygenase


Mass: 23933.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Gene: padAb1, padAb, padAb2, RHA1_ro08166, RHA1_ro10209 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q68YB5, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor
#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol.
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.88→27.95 Å / Num. obs: 76319 / % possible obs: 99.8 % / Redundancy: 13.9 % / CC1/2: 0.979 / Net I/σ(I): 7.1
Reflection shellResolution: 2.88→2.94 Å / Num. unique obs: 4521 / CC1/2: 0.897

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→27.462 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.8 / WRfactor Rfree: 0.28 / WRfactor Rwork: 0.225 / SU B: 0.001 / SU ML: 0 / Average fsc free: 0.945 / Average fsc work: 0.9666 / Cross valid method: THROUGHOUT / ESU R: 0.39 / ESU R Free: 0.484 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.3061 3800 5.008 %RANDOM
Rwork0.2466 72074 --
all0.25 ---
obs-75874 99.212 %-
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: 20.725 Å2
Baniso -1Baniso -2Baniso -3
1--0.822 Å2-0.411 Å2-0 Å2
2---0.822 Å2-0 Å2
3---2.666 Å2
Refinement stepCycle: LAST / Resolution: 2.88→27.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20336 0 20 525 20881
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
2.88-2.9540.4132440.35253330.35555920.910.94299.73180.345
2.954-3.0340.3832560.2951760.29554430.9190.95399.79790.279
3.034-3.1210.4232890.31849610.32452730.9140.95399.56380.303
3.121-3.2150.4032330.36448750.36651330.9240.94799.5130.344
3.215-3.3190.4242500.31846920.32349770.9170.9599.29680.295
3.319-3.4340.3382250.28645690.28848360.9360.95999.13150.268
3.434-3.5610.3282930.27743360.2846370.9420.9799.82750.269
3.561-3.7040.3792190.33542640.33844870.9520.96999.91090.328
3.704-3.8660.3012040.25640850.25843240.9510.97299.19060.243
3.866-4.0510.3012110.22738630.23141360.9550.97298.5010.205
4.051-4.2640.2462130.20636100.20839060.9660.97697.87510.188
4.264-4.5160.2531960.20735220.2137460.9620.97799.25250.195
4.516-4.8190.2161670.15832850.16135020.9720.98598.57220.147
4.819-5.1920.2211560.14830950.15132730.9730.98799.32780.14
5.192-5.6670.2251540.16528640.16830290.9690.98599.63680.159
5.667-6.3020.2411440.17226070.17627520.9720.98599.96370.167
6.302-7.2140.2381150.18923280.19224430.9720.9831000.183
7.214-8.6870.1991060.15619890.15820970.9770.98799.90460.152
8.687-11.7130.214830.13815970.14216800.970.9881000.134
11.713-27.4620.266420.23610230.23710920.9660.97197.52750.227

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