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- PDB-8z4q: The crystal structure of a Hydroquinone Dioxygenase PaD -

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Basic information

Entry
Database: PDB / ID: 8z4q
TitleThe crystal structure of a Hydroquinone Dioxygenase PaD
ComponentsHydroquinone Dioxygenase PaD
KeywordsOXIDOREDUCTASE / Hydroquinone Dioxygenase
Function / homology:
Function and homology information
Biological speciesAspergillus westerdijkiae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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)54,2532
Polymers54,1971
Non-polymers561
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.209, 120.209, 93.305
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#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)
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
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: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M Tris pH 8.0, 25% PEG 1000, 0.1 M Sodium Malonate pH 8.0

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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 EIGER X 9M / Detector: PIXEL / Date: May 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.68→25 Å / Num. obs: 87221 / % possible obs: 99.5 % / Redundancy: 6.3 % / CC1/2: 0.998 / Net I/σ(I): 33.16
Reflection shellResolution: 1.68→1.74 Å / Mean I/σ(I) obs: 2.63 / Num. unique obs: 8727 / CC1/2: 0.866

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→24.56 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.258 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24416 4301 4.9 %RANDOM
Rwork0.21948 ---
obs0.22071 82764 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.753 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.68→24.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 1 467 4211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133879
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173473
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.6475261
X-RAY DIFFRACTIONr_angle_other_deg1.5141.5758040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3465474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11420.92250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72415643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2331539
X-RAY DIFFRACTIONr_chiral_restr0.0970.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02905
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_it1.4521.4761863
X-RAY DIFFRACTIONr_mcbond_other1.451.4751862
X-RAY DIFFRACTIONr_mcangle_it2.032.2082330
X-RAY DIFFRACTIONr_mcangle_other2.0292.212331
X-RAY DIFFRACTIONr_scbond_it2.2091.7322016
X-RAY DIFFRACTIONr_scbond_other2.2091.7332017
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3652.5132925
X-RAY DIFFRACTIONr_long_range_B_refined4.54518.1634593
X-RAY DIFFRACTIONr_long_range_B_other4.43217.7464493
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 294 -
Rwork0.298 5950 -
obs--96.31 %

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