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- PDB-5m22: Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomon... -

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Basic information

Entry
Database: PDB / ID: 5m22
TitleCrystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3
Components
  • Hydroquinone dioxygenase large subunit
  • Hydroquinone dioxygenase small subunit
KeywordsOXIDOREDUCTASE
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 / metal ion binding / : / Hydroquinone dioxygenase small subunit / Hydroquinone dioxygenase large subunit
Function and homology information
Biological speciesSphingomonas sp. TTNP3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 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 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / database_2 / pdbx_initial_refinement_model / 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

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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)227,46612
Polymers227,2428
Non-polymers2234
Water12,196677
1
C: Hydroquinone dioxygenase small subunit
D: Hydroquinone dioxygenase large subunit
hetero molecules

A: Hydroquinone dioxygenase small subunit
B: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7336
Polymers113,6214
Non-polymers1122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
2
A: Hydroquinone dioxygenase small subunit
B: Hydroquinone dioxygenase large subunit
hetero molecules

C: Hydroquinone dioxygenase small subunit
D: Hydroquinone dioxygenase large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7336
Polymers113,6214
Non-polymers1122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area15350 Å2
ΔGint-129 kcal/mol
Surface area34850 Å2
MethodPISA
3
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)113,7336
Polymers113,6214
Non-polymers1122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-125 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.329, 126.090, 92.967
Angle α, β, γ (deg.)90.000, 105.020, 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: Hydroquinone1,2-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: Hydroquinone1,2-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


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


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
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: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.39→47.508 Å / Num. obs: 76541 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 1.97 % / Biso Wilson estimate: 32.845 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.107 / Net I/σ(I): 6.83
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.39-2.530.5261.620.66195.5
2.53-2.710.3852.30.771197.7
2.71-2.920.2453.440.886197.8
2.92-3.20.1565.010.943197.9
3.2-3.580.0957.880.98196.9
3.58-4.130.06611.30.988197.7
4.13-5.040.04715.010.993196.8
5.04-7.090.04913.620.992196.6
7.09-47.5080.03319.030.996193.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
XSCALEdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5M21

5m21


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.897 / SU B: 11.012 / SU ML: 0.241 / SU R Cruickshank DPI: 0.6176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.618 / ESU R Free: 0.294 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 3643 4.8 %RANDOM
Rwork0.1782 ---
obs0.1818 72005 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.81 Å2 / Biso mean: 29.821 Å2 / Biso min: 2.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å21.14 Å2
2---1.25 Å20 Å2
3---1.46 Å2
Refinement stepCycle: final / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15302 0 4 677 15983
Biso mean--25.48 27.51 -
Num. residues----1970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01915702
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.93321339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03451962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96123.35782
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.889152341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.04315129
X-RAY DIFFRACTIONr_chiral_restr0.1010.22250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112443
X-RAY DIFFRACTIONr_mcbond_it1.7722.9877872
X-RAY DIFFRACTIONr_mcangle_it2.8064.4689823
X-RAY DIFFRACTIONr_scbond_it2.1983.0217830
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 258 -
Rwork0.303 5289 -
all-5547 -
obs--97.76 %

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