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- PDB-1o7p: NAPHTHALENE 1,2-DIOXYGENASE, PRODUCT COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1o7p
TitleNAPHTHALENE 1,2-DIOXYGENASE, PRODUCT COMPLEX
Components(NAPHTHALENE 1,2-DIOXYGENASE ...) x 2
KeywordsOXIDOREDUCTASE / NON-HEME IRON DIOXYGENASE / ENZYME-SUBSTRATE COMPLEX / IRON-SULFUR / AROMATIC HYDROCARBON CATABOLISM OXIDOREDUCTASE
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 / (1R, 2S)-CIS 1,2 DIHYDROXY-1,2-DIHYDRONAPHTHALENE / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 1.3Dec 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

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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)73,68814
Polymers72,6332
Non-polymers1,05412
Water7,638424
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)221,06442
Polymers217,9006
Non-polymers3,16336
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)139.673, 139.673, 208.439
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-2182-

HOH

21B-2107-

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 / 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, 436 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-NDH / (1R, 2S)-CIS 1,2 DIHYDROXY-1,2-DIHYDRONAPHTHALENE / (1R,2S)-1,2-DIHYDRONAPHTHALENE-1,2-DIOL


Mass: 162.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O2
#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.: 424 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCOMPONENT OF NAPHTHALENE DIOXYGENASE (NDO) MULTICOMPONENT ENZYME SYSTEM WHICH CATALYZES THE ...COMPONENT OF NAPHTHALENE DIOXYGENASE (NDO) MULTICOMPONENT ENZYME SYSTEM WHICH CATALYZES THE INCORPORATION OF BOTH ATOMS OF MOLECULAR OXYGEN INTO NAPHTHALENE TO FORM CIS-NAPHTHALENE DIHYDRODIOL.

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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 1999 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 56759 / % possible obs: 99.8 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.8
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.8 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 493885 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 32.1

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Processing

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

1eg9


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.934 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2882 5.1 %RANDOM
Rwork0.184 ---
obs-53871 99.5 %-
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: 29.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.3 Å20 Å2
2--0.59 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 56 424 5568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0215257
X-RAY DIFFRACTIONr_bond_other_d0.0010.024560
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9357101
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49215888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1230.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025914
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021119
X-RAY DIFFRACTIONr_nbd_refined0.2190.31080
X-RAY DIFFRACTIONr_nbd_other0.2090.34402
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.2540.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.5440
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.3121
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5720.534
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9961.53167
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.80525066
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.71132090
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3264.52033
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: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.232 210
Rwork0.193 3980
Software
*PLUS
Name: REFMAC / Version: '5.0.36 18/01/2001' / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.799
LS refinement shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 2.001 Å / Rfactor Rfree: 0.232 / Num. reflection Rfree: 210 / Rfactor Rwork: 0.193 / Num. reflection Rwork: 3980 / Total num. of bins used: 20

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