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- PDB-4zxc: Crystal Structure of hydroquinone 1,2-dioxygenase PnpCD in comple... -

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Basic information

Entry
Database: PDB / ID: 4zxc
TitleCrystal Structure of hydroquinone 1,2-dioxygenase PnpCD in complex with Fe3+
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: 3.05 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 / struct_conn
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroquinone dioxygenase small subunit
D: Hydroquinone dioxygenase small subunit
C: Hydroquinone dioxygenase small subunit
B: Hydroquinone dioxygenase small subunit
W: Hydroquinone dioxygenase large subunit
Z: Hydroquinone dioxygenase large subunit
Y: Hydroquinone dioxygenase large subunit
X: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,85910
Polymers226,7488
Non-polymers1122
Water1,874104
1
A: Hydroquinone dioxygenase small subunit
B: Hydroquinone dioxygenase small subunit
W: Hydroquinone dioxygenase large subunit
X: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4305
Polymers113,3744
Non-polymers561
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15240 Å2
ΔGint-99 kcal/mol
Surface area37030 Å2
MethodPISA
2
D: Hydroquinone dioxygenase small subunit
C: Hydroquinone dioxygenase small subunit
Z: Hydroquinone dioxygenase large subunit
Y: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4305
Polymers113,3744
Non-polymers561
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15220 Å2
ΔGint-103 kcal/mol
Surface area37250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.837, 181.743, 186.863
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.: 4
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.: 4
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: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium thiocyanate, 20% w/v PEG 3350

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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: Jun 5, 2014
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: 50659 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rsym value: 0.138 / Net I/σ(I): 28.6
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 7.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZXA

4zxa


Resolution: 3.05→33.12 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2510 5.09 %Random
Rwork0.188 ---
obs0.191 49318 96.4 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 2.15 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.6723 Å20 Å20 Å2
2--22.529 Å20 Å2
3----12.8567 Å2
Refinement stepCycle: LAST / Resolution: 3.05→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15448 0 2 104 15554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115872
X-RAY DIFFRACTIONf_angle_d1.2421556
X-RAY DIFFRACTIONf_dihedral_angle_d17.2545744
X-RAY DIFFRACTIONf_chiral_restr0.0822276
X-RAY DIFFRACTIONf_plane_restr0.0062840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0411-3.09960.34081140.28731958X-RAY DIFFRACTION73
3.0996-3.16280.33961210.27092452X-RAY DIFFRACTION93
3.1628-3.23150.35051340.24822520X-RAY DIFFRACTION94
3.2315-3.30660.29431470.23082546X-RAY DIFFRACTION96
3.3066-3.38920.30341260.21562585X-RAY DIFFRACTION97
3.3892-3.48080.27621440.20192621X-RAY DIFFRACTION98
3.4808-3.58310.27481450.19532595X-RAY DIFFRACTION98
3.5831-3.69860.26721400.19332637X-RAY DIFFRACTION99
3.6986-3.83060.26041290.1832659X-RAY DIFFRACTION98
3.8306-3.98370.23771280.16912581X-RAY DIFFRACTION97
3.9837-4.16470.2271390.16562613X-RAY DIFFRACTION98
4.1647-4.38380.22191520.14952675X-RAY DIFFRACTION99
4.3838-4.65780.20011440.14412645X-RAY DIFFRACTION99
4.6578-5.01630.18771410.14282673X-RAY DIFFRACTION99
5.0163-5.5190.22561480.17232718X-RAY DIFFRACTION99
5.519-6.31280.24361320.19512725X-RAY DIFFRACTION99
6.3128-7.93540.21221520.17952746X-RAY DIFFRACTION100
7.9354-33.12380.20751740.20672859X-RAY DIFFRACTION99

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