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- PDB-5m26: Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomon... -

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Basic information

Entry
Database: PDB / ID: 5m26
TitleCrystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 in complex with methylhydroquinone
Components
  • Hydroquinone dioxygenase large subunit
  • Hydroquinone dioxygenase small subunit
KeywordsOXIDOREDUCTASE / DIOXYGENASE / CUPIN
Function / homologyHydroquinone 1,2-dioxygenase large subunit, N-terminal / Hydroquinone 1,2-dioxygenase large subunit N-terminal / Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / dioxygenase activity / RmlC-like cupin domain superfamily / 2-methylbenzene-1,4-diol / : / Hydroquinone dioxygenase small subunit / Hydroquinone dioxygenase large subunit
Function and homology information
Biological speciesSphingomonas sp. TTNP3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsFerraroni, M. / Da Vela, S. / Scozzafava, A. / Kolvenbach, B. / Corvini, P.F.X.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: The crystal structures of native hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 and of substrate and inhibitor complexes.
Authors: Ferraroni, M. / Da Vela, S. / Kolvenbach, B.A. / Corvini, P.F. / Scozzafava, A.
History
DepositionOct 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Hydroquinone dioxygenase large subunit
C: Hydroquinone dioxygenase small subunit
D: Hydroquinone dioxygenase large subunit
E: Hydroquinone dioxygenase small subunit
F: Hydroquinone dioxygenase large subunit
G: Hydroquinone dioxygenase small subunit
H: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,96216
Polymers227,2428
Non-polymers7208
Water36,6612035
1
A: Hydroquinone dioxygenase small subunit
B: Hydroquinone dioxygenase large subunit
C: Hydroquinone dioxygenase small subunit
D: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9818
Polymers113,6214
Non-polymers3604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Hydroquinone dioxygenase small subunit
F: Hydroquinone dioxygenase large subunit
G: Hydroquinone dioxygenase small subunit
H: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,9818
Polymers113,6214
Non-polymers3604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.406, 125.231, 91.352
Angle α, β, γ (deg.)90.000, 102.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hydroquinone dioxygenase small subunit


Mass: 18571.809 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Hydroquinone 1,2-dioxygenase small subunit / Source: (natural) Sphingomonas sp. TTNP3 (bacteria)
References: UniProt: F8TW82, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Protein
Hydroquinone dioxygenase large subunit


Mass: 38238.789 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Hydroquinone 1,2-dioxygenase large subunit / Source: (natural) Sphingomonas sp. TTNP3 (bacteria)
References: UniProt: F8TW83, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-7DV / 2-methylbenzene-1,4-diol


Mass: 124.137 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2035 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.5 / Details: 14% PEG 3350, 0.35 M MgCl2 and 0.1 M Mes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.694 Å / Num. obs: 149371 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.84 % / Biso Wilson estimate: 24.408 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Net I/σ(I): 10.43
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.9-2.010.6042.720.797194.8
2.01-2.150.3964.220.876197.4
2.15-2.320.2785.710.93197.1
2.32-2.540.2137.020.95197.6
2.54-2.840.1410.070.979198.1
2.84-3.280.08615.040.992198.5
3.28-4.010.06322.010.995198.7
4.01-5.650.04825.840.997199.2
5.65-46.6940.05228.450.997199

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5M21

5m21


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.816 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1533 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.141 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 7452 5 %RANDOM
Rwork0.1604 ---
obs0.1628 141943 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 80.98 Å2 / Biso mean: 21.792 Å2 / Biso min: 5.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0 Å20.68 Å2
2---0.39 Å2-0 Å2
3---0.99 Å2
Refinement stepCycle: final / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15307 0 38 2035 17380
Biso mean--23.35 32.13 -
Num. residues----1963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01915789
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.93521460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59251969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75923.363791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.952152378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.55715131
X-RAY DIFFRACTIONr_chiral_restr0.1020.22257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112518
X-RAY DIFFRACTIONr_mcbond_it1.0731.9717858
X-RAY DIFFRACTIONr_mcangle_it1.6962.9449809
X-RAY DIFFRACTIONr_scbond_it1.662.0967931
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 489 -
Rwork0.257 9855 -
all-10344 -
obs--91.89 %

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