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- PDB-9dr8: Crystal structure of Catechol 1,2-dioxygenase from Burkholderia m... -

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Basic information

Entry
Database: PDB / ID: 9dr8
TitleCrystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Iron bound)
ComponentsCatechol 1,2-dioxygenase
KeywordsHYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Catechol 1 / 2-dioxygenase
Function / homology
Function and homology information


catechol-containing compound catabolic process / catechol 1,2-dioxygenase / catechol 1,2-dioxygenase activity / beta-ketoadipate pathway / ferric iron binding
Similarity search - Function
Catechol 1,2-dioxygenase, proteobacteria / Catechol dioxygenase, N-terminal / Catechol dioxygenase N terminus / Intradiol ring-cleavage dioxygenases signature. / : / Intradiol ring-cleavage dioxygenase, C-terminal / Intradiol ring-cleavage dioxygenase, core / Dioxygenase
Similarity search - Domain/homology
: / catechol 1,2-dioxygenase
Similarity search - Component
Biological speciesBurkholderia multivorans ATCC 17616 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Iron bound)
Authors: Liu, L. / Enayati, P. / Lovell, S. / Buchko, G.W. / Battaile, K.P.
History
DepositionSep 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catechol 1,2-dioxygenase
B: Catechol 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,39113
Polymers69,0372
Non-polymers1,35311
Water16,538918
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9830 Å2
ΔGint-118 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.467, 52.327, 120.396
Angle α, β, γ (deg.)90.00, 92.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Catechol 1,2-dioxygenase / BumuA.00117.a.B1


Mass: 34518.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans ATCC 17616 (bacteria)
Gene: catA / Plasmid: BumuA.00117.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KXJ8, catechol 1,2-dioxygenase

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Non-polymers , 5 types, 929 molecules

#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% (w/v) 4000, 0.2M CaCl2, 0.1M Tris 8.5, BumuA.00107.d.A2.PW32075 at 21.7 mg/mL. plate Liu-S-128 B7. Protein prepared in the presence of FeCl2. Puck: PSL-1602, Cryo: 32% (w/v) 4000, 0.2M CaCl2, 0.1M Tris 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jul 14, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.42→120.28 Å / Num. obs: 135545 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.039 / Rrim(I) all: 0.098 / Χ2: 1 / Net I/σ(I): 9.8 / Num. measured all: 874961
Reflection shellResolution: 1.42→1.46 Å / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.143 / Num. measured all: 66205 / Num. unique obs: 10027 / CC1/2: 0.786 / Rpim(I) all: 0.475 / Rrim(I) all: 1.24 / Χ2: 1.07 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(dev_5449: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→57.68 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1727 6709 4.96 %
Rwork0.1435 --
obs0.145 135355 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→57.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4687 0 74 918 5679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055030
X-RAY DIFFRACTIONf_angle_d0.8076851
X-RAY DIFFRACTIONf_dihedral_angle_d12.8531909
X-RAY DIFFRACTIONf_chiral_restr0.075750
X-RAY DIFFRACTIONf_plane_restr0.012916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.28472520.25084266X-RAY DIFFRACTION100
1.44-1.450.28282120.22934272X-RAY DIFFRACTION99
1.45-1.470.21372160.20224268X-RAY DIFFRACTION100
1.47-1.490.24512430.20094194X-RAY DIFFRACTION100
1.49-1.510.21182290.18344286X-RAY DIFFRACTION100
1.51-1.530.21372480.17194158X-RAY DIFFRACTION100
1.53-1.550.20831990.16164331X-RAY DIFFRACTION100
1.55-1.570.2132210.14884265X-RAY DIFFRACTION100
1.57-1.60.18122290.14594240X-RAY DIFFRACTION100
1.6-1.630.18112180.14364364X-RAY DIFFRACTION100
1.63-1.650.17512020.13724213X-RAY DIFFRACTION100
1.65-1.680.1672290.13744284X-RAY DIFFRACTION100
1.68-1.720.18211940.1374316X-RAY DIFFRACTION100
1.72-1.750.17472170.14044293X-RAY DIFFRACTION100
1.75-1.790.17752120.13814232X-RAY DIFFRACTION100
1.79-1.830.1852450.14754238X-RAY DIFFRACTION100
1.83-1.880.20142360.14944314X-RAY DIFFRACTION100
1.88-1.930.19152470.14244244X-RAY DIFFRACTION100
1.93-1.980.16952250.13464284X-RAY DIFFRACTION100
1.98-2.050.16022240.13454274X-RAY DIFFRACTION100
2.05-2.120.16431930.13624351X-RAY DIFFRACTION100
2.12-2.210.15892090.13384271X-RAY DIFFRACTION100
2.21-2.310.17162180.13034328X-RAY DIFFRACTION100
2.31-2.430.15972380.13214298X-RAY DIFFRACTION100
2.43-2.580.16582380.13194256X-RAY DIFFRACTION100
2.58-2.780.17542170.13914353X-RAY DIFFRACTION100
2.78-3.060.16782370.14074317X-RAY DIFFRACTION100
3.06-3.50.17671990.14344351X-RAY DIFFRACTION100
3.5-4.410.14452240.134333X-RAY DIFFRACTION99
4.41-57.680.16642380.15994452X-RAY DIFFRACTION100

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