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- PDB-8z4r: The crystal structure of a Hydroquinone Dioxygenase PaD with substrate -

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Basic information

Entry
Database: PDB / ID: 8z4r
TitleThe crystal structure of a Hydroquinone Dioxygenase PaD with substrate
ComponentsHydroquinone Dioxygenase PaD
KeywordsOXIDOREDUCTASE / Hydroquinone Dioxygenase
Function / homology: / ACETATE ION / : / FORMIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesAspergillus westerdijkiae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsLiu, Z.W. / Huang, J.-W. / Wang, Y.X. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Substrate specificity of a branch of aromatic dioxygenases determined by three distinct motifs.
Authors: Cui, C. / Yang, L.J. / Liu, Z.W. / Shu, X. / Zhang, W.W. / Gao, Y. / Wang, Y.X. / Wang, T. / Chen, C.C. / Guo, R.T. / Gao, S.S.
History
DepositionApr 17, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroquinone Dioxygenase PaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,08713
Polymers54,1971
Non-polymers89012
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.177, 120.177, 92.919
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Hydroquinone Dioxygenase PaD


Mass: 54196.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus westerdijkiae (mold) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 6 types, 436 molecules

#2: Chemical ChemComp-A1D7Y / 2-methoxy-6-methyl-benzene-1,4-diol / 62AA03E1HR


Mass: 154.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M HEPES 7.0; 24% PEG Smear Medium; 7% Tacsimate 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.81→25 Å / Num. obs: 69612 / % possible obs: 99.6 % / Redundancy: 5.8 % / CC1/2: 0.999 / Net I/σ(I): 29.4
Reflection shellResolution: 1.81→1.87 Å / Num. unique obs: 6931 / CC1/2: 0.885

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→24.53 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.775 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22491 3580 5.1 %RANDOM
Rwork0.18629 ---
obs0.18833 65962 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.014 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.04 Å2-0 Å2
2--0.09 Å20 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.81→24.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 57 427 4240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133933
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173533
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.655313
X-RAY DIFFRACTIONr_angle_other_deg1.4771.5798169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17820.92250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40415644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1341539
X-RAY DIFFRACTIONr_chiral_restr0.0990.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02912
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_it3.2233.4561872
X-RAY DIFFRACTIONr_mcbond_other3.2033.4551872
X-RAY DIFFRACTIONr_mcangle_it3.7875.1542337
X-RAY DIFFRACTIONr_mcangle_other3.7875.1562338
X-RAY DIFFRACTIONr_scbond_it4.1113.8652061
X-RAY DIFFRACTIONr_scbond_other4.113.8672062
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.575.642971
X-RAY DIFFRACTIONr_long_range_B_refined6.69641.7394643
X-RAY DIFFRACTIONr_long_range_B_other6.66841.2044550
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 318 -
Rwork0.287 4734 -
obs--97.21 %

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