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- PDB-4huz: 2,6-Dichloro-p-hydroquinone 1,2-Dioxygenase -

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Basic information

Entry
Database: PDB / ID: 4huz
Title2,6-Dichloro-p-hydroquinone 1,2-Dioxygenase
Components2,6-dichloro-p-hydroquinone 1,2-dioxygenase
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
2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
: / 2,6-dichloro-p-hydroquinone 1,2-dioxygenase
Similarity search - Component
Biological speciesSphingobium chlorophenolicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHayes, R.P. / Nissen, M.S. / Green, A.R. / Lewis, K.M. / Xun, L. / Kang, C.
CitationJournal: Mol.Microbiol. / Year: 2013
Title: Structural characterization of 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA) from Sphingobium chlorophenolicum, a new type of aromatic ring-cleavage enzyme.
Authors: Hayes, R.P. / Green, A.R. / Nissen, M.S. / Lewis, K.M. / Xun, L. / Kang, C.
History
DepositionNov 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Sep 20, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,6-dichloro-p-hydroquinone 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7143
Polymers36,5621
Non-polymers1522
Water181
1
A: 2,6-dichloro-p-hydroquinone 1,2-dioxygenase
hetero molecules

A: 2,6-dichloro-p-hydroquinone 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4276
Polymers73,1232
Non-polymers3044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3050 Å2
ΔGint-73 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.317, 65.317, 294.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 2,6-dichloro-p-hydroquinone 1,2-dioxygenase


Mass: 36561.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium chlorophenolicum (bacteria)
Gene: pcpA / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ZBB0, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.3 Å3/Da / Density % sol: 71.38 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 85 mM HEPES, 85 mM NaCl, 1.36 M (NH4)2SO4 and 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 23194 / Num. obs: 23194 / % possible obs: 89 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.087
Reflection shellResolution: 2.4→2.44 Å / % possible all: 25.1

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3oaj

3oaj


Resolution: 2.6→48.873 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 31.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 1750 8.66 %
Rwork0.1957 --
obs0.1999 20202 97.57 %
all-18745 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.7233 Å20 Å2-0 Å2
2--17.7233 Å2-0 Å2
3----35.4466 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 6 1 2558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162631
X-RAY DIFFRACTIONf_angle_d1.2043564
X-RAY DIFFRACTIONf_dihedral_angle_d15.734950
X-RAY DIFFRACTIONf_chiral_restr0.083364
X-RAY DIFFRACTIONf_plane_restr0.005471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.67040.40381070.36631150X-RAY DIFFRACTION83
2.6704-2.74890.38891280.32151327X-RAY DIFFRACTION92
2.7489-2.83770.36441310.29941372X-RAY DIFFRACTION97
2.8377-2.93910.34121300.28881390X-RAY DIFFRACTION99
2.9391-3.05670.37411360.27951419X-RAY DIFFRACTION99
3.0567-3.19580.31251330.271415X-RAY DIFFRACTION99
3.1958-3.36430.31451350.21841420X-RAY DIFFRACTION99
3.3643-3.5750.28021380.19891442X-RAY DIFFRACTION100
3.575-3.85090.26121390.20031463X-RAY DIFFRACTION100
3.8509-4.23820.20711360.16781436X-RAY DIFFRACTION100
4.2382-4.85110.20421400.14971470X-RAY DIFFRACTION100
4.8511-6.110.22251440.16931514X-RAY DIFFRACTION100
6.11-48.8820.1891530.17981634X-RAY DIFFRACTION100

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