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- PDB-1uuw: NAPHTHALENE 1,2-DIOXYGENASE WITH NITRIC OXIDE BOUND IN THE ACTIVE... -

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Basic information

Entry
Database: PDB / ID: 1uuw
TitleNAPHTHALENE 1,2-DIOXYGENASE WITH NITRIC OXIDE BOUND IN THE ACTIVE SITE.
Components(NAPHTHALENE 1,2-DIOXYGENASE ...) x 2
KeywordsOXIDOREDUCTASE / NON-HEME IRON DIOXYGENASE / ENZYME-SUBSTRATE COMPLEX / AROMATIC HYDROCARBONS CATABOLISM / METAL-BINDING / IRON-SULFUR / IRON / 2FE-2S / DIOXYGENASE / NAD / PLASMID
Function / homology
Function and homology information


naphthalene 1,2-dioxygenase / naphthalene 1,2-dioxygenase activity / : / dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 ...Ring-hydroxylating dioxygenase, alpha subunit NdoB-like, C-terminal / Ring hydroxylating beta subunit / Ring-hydroxylating dioxygenase beta subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Nuclear Transport Factor 2; Chain: A, - #50 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / NITRIC OXIDE / Naphthalene 1,2-dioxygenase system, large oxygenase component / Naphthalene 1,2-dioxygenase system, small oxygenase component
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKarlsson, A. / Parales, J.V. / Parales, R.E. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2005
Title: No Binding to Naphthalene Dioxygenase.
Authors: Karlsson, A. / Parales, J.V. / Parales, R.E. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
History
DepositionJan 11, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT
B: NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0877
Polymers72,6332
Non-polymers4545
Water6,269348
1
A: NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT
B: NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT
hetero molecules

A: NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT
B: NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT
hetero molecules

A: NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT
B: NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,26221
Polymers217,9006
Non-polymers1,36115
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area33070 Å2
ΔGint-155.5 kcal/mol
Surface area76720 Å2
MethodPQS
Unit cell
Length a, b, c (Å)140.556, 140.556, 210.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-2090-

HOH

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Components

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NAPHTHALENE 1,2-DIOXYGENASE ... , 2 types, 2 molecules AB

#1: Protein NAPHTHALENE 1,2-DIOXYGENASE ALPHA SUBUNIT / NAPHTHALENE 1 / 2-DIOXYGENASE ISP ALPHA


Mass: 49664.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: NCIB9816-4 / Plasmid: PDTG14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P0A110, naphthalene 1,2-dioxygenase
#2: Protein NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT / NAPHTHALENE 1 / 2-DIOXYGENASE ISP BETA


Mass: 22969.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: NCIB9816-4 / Plasmid: PDTG14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P0A112, naphthalene 1,2-dioxygenase

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Non-polymers , 5 types, 353 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Chemical ChemComp-FE / FE (III) ION / Iron


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYTIC ACTIVITY: NAPHTHALENE + NADH + O(2) = (1R,2S)-1,2- DIHYDRONAPHTHALENE-1,2-DIOL + NAD(+).

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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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growpH: 6
Details: AMMONIUM SULPHATE 2M, MES, 0.1M, DIOXANE 2-3%, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 32084 / % possible obs: 92.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.2 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EG9

1eg9


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.185 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1041 3.2 %RANDOM
Rwork0.198 ---
obs-31759 91.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 26.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 17 348 5453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215223
X-RAY DIFFRACTIONr_bond_other_d0.0010.024552
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9297065
X-RAY DIFFRACTIONr_angle_other_deg0.849310585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4433638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.97615888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025906
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021115
X-RAY DIFFRACTIONr_nbd_refined0.2220.31063
X-RAY DIFFRACTIONr_nbd_other0.2080.34279
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.5384
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0120.52
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.323
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.3115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.360.527
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6361.53168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20325066
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.58732055
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.694.51997
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.202 82
Rwork0.202 2377

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