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- PDB-5m21: Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomon... -

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Basic information

Entry
Database: PDB / ID: 5m21
TitleCrystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 with 4-hydroxybenzoate bound
Components
  • Hydroquinone dioxygenase large subunit
  • Hydroquinone dioxygenase small subunit
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / dioxygenase activity / metal ion binding
Similarity search - Function
Hydroquinone 1,2-dioxygenase large subunit, N-terminal / Hydroquinone 1,2-dioxygenase large subunit N-terminal / RmlC-like cupin domain superfamily
Similarity search - Domain/homology
: / P-HYDROXYBENZOIC ACID / Hydroquinone dioxygenase small subunit / Hydroquinone dioxygenase large subunit
Similarity search - Component
Biological speciesSphingomonas sp. TTNP3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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

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)228,01816
Polymers227,2428
Non-polymers7768
Water20,5551141
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)114,0098
Polymers113,6214
Non-polymers3884
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)114,0098
Polymers113,6214
Non-polymers3884
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area16170 Å2
ΔGint-128 kcal/mol
Surface area34080 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)114,0098
Polymers113,6214
Non-polymers3884
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15970 Å2
ΔGint-128 kcal/mol
Surface area34810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.782, 124.869, 92.371
Angle α, β, γ (deg.)90.000, 105.150, 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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1141 / 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: 43.44 %
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: 1.99→29.856 Å / Num. obs: 130301 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.32 % / Biso Wilson estimate: 30.103 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.117 / Net I/σ(I): 8.86
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.99-2.110.5832.450.846188.9
2.11-2.250.4033.60.889199.3
2.25-2.430.3024.510.931199.4
2.43-2.660.2225.890.952199.4
2.66-2.970.13590.983199.5
2.97-3.430.09213.480.991199.6
3.43-4.190.07118.350.993199.3
4.19-5.860.05920.750.994199.6
5.86-29.8560.05922.960.995198.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZXA

4zxa


Resolution: 1.99→29.8 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.872 / SU ML: 0.157 / SU R Cruickshank DPI: 0.1968 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.181 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 6614 5.1 %RANDOM
Rwork0.1793 ---
obs0.1824 123544 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 88.29 Å2 / Biso mean: 27.432 Å2 / Biso min: 11.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å2-0.19 Å2
2---1.04 Å2-0 Å2
3---2.61 Å2
Refinement stepCycle: final / Resolution: 1.99→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15386 0 44 1141 16571
Biso mean--32.67 32.47 -
Num. residues----1976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01915838
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.93121526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04351974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19623.367787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.305152371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.40615129
X-RAY DIFFRACTIONr_chiral_restr0.120.22267
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112673
X-RAY DIFFRACTIONr_mcbond_it2.0352.6127902
X-RAY DIFFRACTIONr_mcangle_it2.8723.9049865
X-RAY DIFFRACTIONr_scbond_it2.8142.787936
LS refinement shellResolution: 1.994→2.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 456 -
Rwork0.313 8135 -
all-8591 -
obs--88.31 %

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