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- PDB-2ei0: Anaerobic Crystal Structure Analysis of 1,2-dihydroxynaphthalene ... -

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Basic information

Entry
Database: PDB / ID: 2ei0
TitleAnaerobic Crystal Structure Analysis of 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. strain C18 complexed with 3,4-dihydroxybiphenyl
Components1,2-dihydroxynaphthalene dioxygenase
KeywordsOXIDOREDUCTASE / extradiol dioxygenase / protein substrate complex
Function / homology
Function and homology information


1,2-dihydroxynaphthalene dioxygenase / 1,2-dihydroxynaphthalene dioxygenase activity / naphthalene catabolic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferrous iron binding
Similarity search - Function
Dihydroxybiphenyl dioxygenase BphC D1 / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 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 ...Dihydroxybiphenyl dioxygenase BphC D1 / Extradiol ring-cleavage dioxygenase, class I /II / Extradiol ring-cleavage dioxygenases signature. / 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
1,1'-BIPHENYL-3,4-DIOL / : / 1,2-dihydroxynaphthalene dioxygenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNeau, D.B. / Kelker, M.S. / Colbert, C.L. / Bolin, J.T.
CitationJournal: To be Published
Title: Structural explanation for success and failure in the enzymatic ring-cleavage of 3,4 dihydroxybiphenyl and related PCB metabolites
Authors: Neau, D.B. / Kelker, M.S. / Maaroufi, H. / Colbert, C.L. / Eltis, L.D. / Bolin, J.T.
History
DepositionMar 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 / _struct_conn.ptnr2_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

Downloads & links

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Assembly

Deposited unit
A: 1,2-dihydroxynaphthalene dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7167
Polymers33,9861
Non-polymers7316
Water6,287349
1
A: 1,2-dihydroxynaphthalene dioxygenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)277,73156
Polymers271,8848
Non-polymers5,84748
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area34090 Å2
ΔGint-379 kcal/mol
Surface area79080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.870, 117.870, 121.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 1,2-dihydroxynaphthalene dioxygenase


Mass: 33985.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: C18 / Gene: doxg / Plasmid: pHMPVDG / Production host: Pseudomonas putida (bacteria) / Strain (production host): KT2442
References: UniProt: P0A108, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen

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Non-polymers , 5 types, 355 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BP7 / 1,1'-BIPHENYL-3,4-DIOL / 3,4-DIHYDROXYBIPHENYL


Mass: 186.207 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H10O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.11 Å3/Da / Density % sol: 60.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8M NaCl, 0.1M MgCl2, 0.1M Hepes, anaerobic crystallization, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.99 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 49031 / % possible obs: 100 % / Redundancy: 8.9 % / Rsym value: 0.056
Reflection shellHighest resolution: 1.6 Å / Rsym value: 0.738 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HAN

1han


Resolution: 1.6→49.15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.259 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17562 2622 5.1 %RANDOM
Rwork0.15978 ---
obs0.16059 49031 91.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.069 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 50 349 2673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212375
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1691.9553214
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86723.59117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44515366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2731514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021871
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.21092
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21585
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6361.51452
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.96722244
X-RAY DIFFRACTIONr_scbond_it1.52731080
X-RAY DIFFRACTIONr_scangle_it2.3554.5970
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 171 -
Rwork0.231 3067 -
obs--78.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75130.2326-0.03290.85-0.11260.8515-0.0322-0.07060.15580.0771-0.0173-0.0462-0.1916-0.03210.04950.055-0.0076-0.0289-0.0169-0.03450.06486.52737.0616.055
20.5182-0.13960.13860.3001-0.17280.54-0.0287-0.10460.06870.06720.0024-0.0232-0.0814-0.05130.02630.0473-0.0099-0.02220.0206-0.03610.03244.99527.81224.964
30.4503-0.26120.03790.5184-0.13670.3884-0.006-0.01550.06980.0171-0.0261-0.1175-0.04440.06550.03210.0232-0.0299-0.02680.0166-0.00990.066520.95823.40613.943
40.3674-0.44060.72630.5298-0.81563.45510.0535-0.38990.29930.0579-0.4826-0.1506-0.42431.0650.4290.1434-0.1275-0.06810.16260.0450.195930.65729.21614.184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 445 - 44
2X-RAY DIFFRACTION2AA45 - 17345 - 173
3X-RAY DIFFRACTION3AA174 - 290174 - 290
4X-RAY DIFFRACTION4AA291 - 295291 - 295

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