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- PDB-4zxd: Crystal Structure of hydroquinone 1,2-dioxygenase PnpCD -

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Basic information

Entry
Database: PDB / ID: 4zxd
TitleCrystal Structure of hydroquinone 1,2-dioxygenase PnpCD
Components
  • Hydroquinone dioxygenase large subunit
  • Hydroquinone dioxygenase small subunit
KeywordsOXIDOREDUCTASE / dioxygenase / cuipin / hydroquinone pathway
Function / homologyHydroquinone 1,2-dioxygenase large subunit, N-terminal / Hydroquinone 1,2-dioxygenase large subunit N-terminal / dioxygenase activity / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / Hydroquinone dioxygenase large subunit / Hydroquinone dioxygenase small subunit
Function and homology information
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.052 Å
AuthorsLiu, S. / Su, T. / Zhang, C. / Gu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31070655 China
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure of PnpCD, a Two-subunit Hydroquinone 1,2-Dioxygenase, Reveals a Novel Structural Class of Fe2+-dependent Dioxygenases.
Authors: Liu, S. / Su, T. / Zhang, C. / Zhang, W.M. / Zhu, D. / Su, J. / Wei, T. / Wang, K. / Huang, Y. / Guo, L. / Xu, S. / Zhou, N.Y. / Gu, L.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroquinone dioxygenase small subunit
B: Hydroquinone dioxygenase small subunit
W: Hydroquinone dioxygenase large subunit
X: Hydroquinone dioxygenase large subunit


Theoretical massNumber of molelcules
Total (without water)113,3744
Polymers113,3744
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14660 Å2
ΔGint-89 kcal/mol
Surface area37140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.199, 114.012, 158.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hydroquinone dioxygenase small subunit


Mass: 18308.932 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (strain WBC-3) (bacteria)
Strain: WBC-3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1I210
#2: Protein Hydroquinone dioxygenase large subunit


Mass: 38377.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (strain WBC-3) (bacteria)
Strain: WBC-3 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C1I209
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.8 M Ammonium citrate dibasic, 0.1 M Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 21998 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rsym value: 0.131 / Net I/σ(I): 19.3
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 4.6 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZXA

4zxa


Resolution: 3.052→38.694 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 1129 5.15 %Random
Rwork0.2018 ---
obs0.2044 21924 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.052→38.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7659 0 0 19 7678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017871
X-RAY DIFFRACTIONf_angle_d1.40510688
X-RAY DIFFRACTIONf_dihedral_angle_d17.6162850
X-RAY DIFFRACTIONf_chiral_restr0.0511126
X-RAY DIFFRACTIONf_plane_restr0.0081407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0521-3.1910.33831550.25122517X-RAY DIFFRACTION99
3.191-3.35910.30091500.22972519X-RAY DIFFRACTION98
3.3591-3.56940.25871420.20252532X-RAY DIFFRACTION99
3.5694-3.84480.2661360.19092576X-RAY DIFFRACTION99
3.8448-4.23130.24991320.19212596X-RAY DIFFRACTION100
4.2313-4.84260.21651470.16782606X-RAY DIFFRACTION100
4.8426-6.09730.21441340.20462663X-RAY DIFFRACTION100
6.0973-38.69760.25581330.21492786X-RAY DIFFRACTION100

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