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- PDB-1o7m: NAPHTHALENE 1,2-DIOXYGENASE, BINARY COMPLEX WITH DIOXYGEN -

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Basic information

Entry
Database: PDB / ID: 1o7m
TitleNAPHTHALENE 1,2-DIOXYGENASE, BINARY COMPLEX WITH DIOXYGEN
Components(NAPHTHALENE 1,2-DIOXYGENASE ...) x 2
KeywordsOXIDOREDUCTASE / NON-HEME IRON DIOXYGENASE / ENZYME-SUBSTRATE COMPLEX / IRON-SULFUR / AROMATIC HYDROCARBON CATABOLISM
Function / homology
Function and homology information


: / naphthalene 1,2-dioxygenase / naphthalene 1,2-dioxygenase activity / 3-phenylpropionate catabolic process / catabolic process / 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] domain / Rieske [2Fe-2S] iron-sulphur 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 / OXYGEN MOLECULE / Naphthalene 1,2-dioxygenase system, large oxygenase component / Naphthalene 1,2-dioxygenase system, small oxygenase component / 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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsKarlsson, A. / Parales, J.V. / Parales, R.E. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
CitationJournal: Science / Year: 2003
Title: Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron
Authors: Karlsson, A. / Parales, J.V. / Parales, R.E. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
History
DepositionNov 11, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 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)73,55814
Polymers72,6332
Non-polymers92412
Water9,962553
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)220,67342
Polymers217,9006
Non-polymers2,77336
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
MethodPQS
Unit cell
Length a, b, c (Å)140.277, 140.277, 208.754
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
11A-2253-

HOH

DetailsTHE ACTIVE ENZYME IS A ALPHA3 BETA3 HEXAMER GENERATEDBY THE THREEFOLD

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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 / NDOB / NAHAC


Mass: 49664.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: NCIB 9816-4 / Plasmid: PDTG141 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3)
References: UniProt: P23094, UniProt: P0A110*PLUS, naphthalene 1,2-dioxygenase
#2: Protein NAPHTHALENE 1,2-DIOXYGENASE BETA SUBUNIT / NAPHTHALENE 1 / 2-DIOXYGENASE ISP BETA / NDOC / NAHAD


Mass: 22969.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Strain: NCIB 9816-4 / Plasmid: PDTG141 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3)
References: UniProt: P23095, UniProt: P0A112*PLUS, naphthalene 1,2-dioxygenase

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Non-polymers , 6 types, 565 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#7: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growpH: 6
Details: AMMONIUM SULPHATE 2M, MES 0.1M, DIOXANE 2-3%, pH 6.00
Crystal grow
*PLUS
Temperature: 8 ℃ / Method: vapor diffusion / Details: Carredano, E., (2000) J. Mol. Biol., 296, 701.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
32-3 %dioxane1reservoir
450 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54
DetectorType: RIGAKU MSC / Detector: IMAGE PLATE / Date: Dec 15, 2001 / Details: CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 80092 / % possible obs: 94 % / Redundancy: 3.67 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.2
Reflection shellResolution: 1.75→1.79 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 2.2 / % possible all: 86.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 293928
Reflection shell
*PLUS
% possible obs: 86.5 %

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Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EG9

1eg9


Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.611 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ASN 363 AND MET 366 HAVE BEEN MODELLED WITH DOUBLE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 771 1 %RANDOM
Rwork0.178 ---
obs-77729 98.9 %-
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: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5089 0 46 553 5688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215252
X-RAY DIFFRACTIONr_bond_other_d0.0010.024557
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.9327091
X-RAY DIFFRACTIONr_angle_other_deg1.228310600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0453638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12715891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025914
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021115
X-RAY DIFFRACTIONr_nbd_refined0.2390.31084
X-RAY DIFFRACTIONr_nbd_other0.2170.34461
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.330.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.51007
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.120.53
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.338
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.3130
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.578
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8141.53168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51425069
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.26332084
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.624.52020
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: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.305 46
Rwork0.248 5479
Software
*PLUS
Name: REFMAC / Version: '5.0.36 18/01/2001' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.188 / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.629
LS refinement shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.795 Å / Rfactor Rfree: 0.305 / Num. reflection Rfree: 46 / Rfactor Rwork: 0.248 / Num. reflection Rwork: 5479 / Total num. of bins used: 20

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