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- PDB-2ei2: Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxyg... -

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Basic information

Entry
Database: PDB / ID: 2ei2
TitleCrystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxygenase from Pseudomonas sp. stain C18
Components1,2-dihydroxynaphthalene dioxygenase
KeywordsOXIDOREDUCTASE / extradiol dioxygenase
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
: / 1,2-dihydroxynaphthalene dioxygenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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_ref_seq_dif / 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_ref_seq_dif.details / _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)34,2365
Polymers33,9721
Non-polymers2644
Water4,810267
1
A: 1,2-dihydroxynaphthalene dioxygenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)273,88740
Polymers271,7728
Non-polymers2,11532
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 area26890 Å2
ΔGint-294 kcal/mol
Surface area83140 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.390, 118.390, 120.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein 1,2-dihydroxynaphthalene dioxygenase


Mass: 33971.531 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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 60.45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8M NaCl, 0.1M MgCl2, 0.1M Hepes, naerobic 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 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.69→48.97 Å / Num. obs: 46344 / % possible obs: 97.1 % / Redundancy: 9.7 % / Rsym value: 0.088
Reflection shellHighest resolution: 1.69 Å / Rsym value: 0.646 / % possible all: 97.6

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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: PDB entry 1HAN

1han


Resolution: 1.69→48.97 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.064 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18629 2048 4.9 %RANDOM
Rwork0.16135 ---
obs0.1626 39685 87.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.69→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 14 267 2649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212430
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9423288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8615298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30623.644118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9415386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5741514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021891
X-RAY DIFFRACTIONr_nbd_refined0.2060.31006
X-RAY DIFFRACTIONr_nbtor_refined0.3170.51619
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.5374
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.526
X-RAY DIFFRACTIONr_mcbond_it0.7991.51515
X-RAY DIFFRACTIONr_mcangle_it1.09922355
X-RAY DIFFRACTIONr_scbond_it1.83631052
X-RAY DIFFRACTIONr_scangle_it2.624.5933
LS refinement shellResolution: 1.692→1.736 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 100 -
Rwork0.222 2392 -
obs--72.27 %
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)
11.13710.25390.05390.86370.11251.7447-0.0363-0.08290.31340.0501-0.0325-0.006-0.3944-0.03530.06880.1331-0.0154-0.04930.0096-0.05920.12286.527137.059816.0554
20.8562-0.09680.12560.5737-0.16131.0125-0.0319-0.18620.13580.1507-0.0083-0.0385-0.1724-0.06170.04020.1077-0.0235-0.04130.0519-0.06440.06084.995327.812124.9641
30.8465-0.1790.02820.8009-0.10220.9629-0.0005-0.07260.11210.0664-0.037-0.1883-0.16520.18680.03750.0597-0.0644-0.05280.0533-0.02120.089720.958323.406313.9435
46.9566-5.00063.26889.7331-5.59093.2473-0.0274-0.31480.68190.6808-0.0596-0.664-0.25380.11950.08690.2494-0.1482-0.1130.2885-0.13630.283130.657529.215914.1842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 444 - 44
2X-RAY DIFFRACTION2AA45 - 17345 - 173
3X-RAY DIFFRACTION3AA174 - 290174 - 290
4X-RAY DIFFRACTION4AA291 - 302291 - 302

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