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- PDB-2ei1: Anaerobic Crystal Structure Analysis of the 1,2-dihydroxynaphthal... -

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Basic information

Entry
Database: PDB / ID: 2ei1
TitleAnaerobic Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxygeanse of Pseudomonas sp. strain C18 complexes to 1,2-dihydroxynaphthalene
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
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
NAPHTHALENE-1,2-DIOL / : / 1,2-dihydroxynaphthalene dioxygenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 1.2Sep 9, 2020Group: Advisory / Derived calculations / Structure summary
Category: pdbx_unobs_or_zero_occ_atoms / struct ...pdbx_unobs_or_zero_occ_atoms / struct / struct_conn / struct_site
Item: _struct.title / _struct_conn.ptnr1_auth_comp_id ..._struct.title / _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
Revision 1.3Oct 25, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,3185
Polymers33,9861
Non-polymers3324
Water5,044280
1
A: 1,2-dihydroxynaphthalene dioxygenase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)274,54440
Polymers271,8848
Non-polymers2,65932
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 area27530 Å2
ΔGint-229 kcal/mol
Surface area78330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.848, 117.848, 120.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-1869-

HOH

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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, 284 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-D1N / NAPHTHALENE-1,2-DIOL / 1,2-DIHYDROXYNAPHTHALENE


Mass: 160.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 280 / 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: 3.09 Å3/Da / Density % sol: 60.17 %
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 7, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 64402 / % possible obs: 99.3 % / Redundancy: 13.7 % / Rsym value: 0.063
Reflection shellHighest resolution: 1.52 Å / Rsym value: 0.633 / % possible all: 93.7

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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: 1.52→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.836 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17994 3252 5.1 %RANDOM
Rwork0.17147 ---
obs0.17191 60838 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.52→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 20 280 2625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212396
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9443241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2475291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9423.644118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89215381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0031514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021863
X-RAY DIFFRACTIONr_nbd_refined0.1920.21033
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21597
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.211
X-RAY DIFFRACTIONr_mcbond_it0.6861.51488
X-RAY DIFFRACTIONr_mcangle_it1.00422301
X-RAY DIFFRACTIONr_scbond_it1.51731067
X-RAY DIFFRACTIONr_scangle_it2.2624.5940
LS refinement shellResolution: 1.524→1.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 231 -
Rwork0.253 4117 -
obs--91.77 %
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)
10.85690.28060.00120.4838-0.03380.7419-0.0512-0.0750.2190.0262-0.0241-0.0376-0.1889-0.03080.07530.0764-0.007-0.0533-0.0368-0.04250.07376.527137.059816.0554
20.5448-0.07920.09240.3872-0.07770.4797-0.0207-0.12270.09710.0969-0.0037-0.0223-0.0915-0.03890.02450.0546-0.0122-0.0420.0082-0.04670.01924.995327.812124.9641
30.4264-0.1909-0.01340.41540.01590.5815-0.0131-0.03880.07010.0144-0.0219-0.1224-0.07950.0940.0350.0219-0.0389-0.0460.0021-0.01180.054920.958323.406313.9435
40.91722.519-0.81898.3401-3.03631.1670.0999-0.82110.2743-0.6309-0.6251-0.62860.19160.31410.52520.1945-0.0028-0.00160.2026-0.00080.199730.657529.215914.1842
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 - 302291 - 302

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