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- PDB-8iq8: Crystal structure of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (... -

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Basic information

Entry
Database: PDB / ID: 8iq8
TitleCrystal structure of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (DHPAO) from Acinetobacter baumannii
Components3,4-dihydroxyphenylacetate 2,3-dioxygenase
KeywordsOXIDOREDUCTASE / extradiol dioxygenase
Function / homology3,4-dihydroxyphenylacetate 2,3-dioxygenase / 3,4-dihydroxyphenylacetate 2,3-dioxygenase activity / 3,4-dihydroxyphenylacetate 2,3-dioxygenase / Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B / Catalytic LigB subunit of aromatic ring-opening dioxygenase / ferrous iron binding / 3,4-dihydroxyphenylacetate 2,3-dioxygenase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChitnumsub, P. / Maenpuen, S.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Other governmentP20-50077 Thailand
CitationJournal: Arch.Biochem.Biophys. / Year: 2023
Title: Structure and biochemical characterization of an extradiol 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Acinetobacter baumannii.
Authors: Pimviriyakul, P. / Buttranon, S. / Soithongcharoen, S. / Supawatkon, C. / Disayabootr, K. / Watthaisong, P. / Tinikul, R. / Jaruwat, A. / Chaiyen, P. / Chitnumsub, P. / Maenpuen, S.
History
DepositionMar 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3,4-dihydroxyphenylacetate 2,3-dioxygenase
B: 3,4-dihydroxyphenylacetate 2,3-dioxygenase
C: 3,4-dihydroxyphenylacetate 2,3-dioxygenase
D: 3,4-dihydroxyphenylacetate 2,3-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,6198
Polymers129,5274
Non-polymers924
Water16,340907
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Homotetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-103 kcal/mol
Surface area39310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.433, 62.840, 135.952
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3,4-dihydroxyphenylacetate 2,3-dioxygenase


Mass: 32381.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: hpaD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E1FP33
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 4
Details: 0.1 M PCB buffer pH4 and 25% w/v PEG1500 (Hampton Research kit)
PH range: 4-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Aug 4, 2017
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.77→21.03 Å / Num. obs: 147453 / % possible obs: 97.7 % / Redundancy: 4.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.047 / Rrim(I) all: 0.109 / Χ2: 0.99 / Net I/σ(I): 11.4 / Num. measured all: 667103
Reflection shellResolution: 1.77→1.81 Å / % possible obs: 78.5 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.169 / Num. measured all: 9963 / Num. unique obs: 5851 / CC1/2: 0.92 / Rpim(I) all: 0.149 / Rrim(I) all: 0.226 / Χ2: 1.11 / Net I/σ(I) obs: 5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
PHASERphasing
PROTEUM PLUSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→21.04 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.875 / SU B: 3.15 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25463 14290 10.2 %RANDOM
Rwork0.22501 ---
obs0.22805 126494 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.843 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.03 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→21.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9000 0 4 907 9911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139369
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158507
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.63512698
X-RAY DIFFRACTIONr_angle_other_deg1.3561.57819623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90751148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10422.543527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.202151555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4351555
X-RAY DIFFRACTIONr_chiral_restr0.0730.21160
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210797
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022257
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7970.8064568
X-RAY DIFFRACTIONr_mcbond_other0.7970.8054567
X-RAY DIFFRACTIONr_mcangle_it1.3931.2035724
X-RAY DIFFRACTIONr_mcangle_other1.3931.2045725
X-RAY DIFFRACTIONr_scbond_it1.1520.9594801
X-RAY DIFFRACTIONr_scbond_other1.1520.964802
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9011.3856975
X-RAY DIFFRACTIONr_long_range_B_refined3.4169.86510991
X-RAY DIFFRACTIONr_long_range_B_other3.2239.51510747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.508 879 -
Rwork0.495 8102 -
obs--83.65 %

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