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- PDB-4hm8: Naphthalene 1,2-Dioxygenase bound to thioanisole -

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Basic information

Entry
Database: PDB / ID: 4hm8
TitleNaphthalene 1,2-Dioxygenase bound to thioanisole
Components(Naphthalene 1,2-dioxygenase subunit ...) x 2
KeywordsOxidoreductase/Oxidoreductase inhibitor / Oxidoreductase-Oxidoreductase inhibitor complex
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
(methylsulfanyl)benzene / : / FE2/S2 (INORGANIC) CLUSTER / Naphthalene 1,2-dioxygenase system, large oxygenase component / Naphthalene 1,2-dioxygenase system, small oxygenase component
Similarity search - Component
Biological speciesPseudomonas sp. C18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFerraro, D.J. / Ramaswamy, S.
CitationJournal: Iucrj / Year: 2017
Title: One enzyme, many reactions: structural basis for the various reactions catalyzed by naphthalene 1,2-dioxygenase.
Authors: Ferraro, D.J. / Okerlund, A. / Brown, E. / Ramaswamy, S.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Non-polymer description
Revision 1.2Sep 18, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Naphthalene 1,2-dioxygenase subunit alpha
B: Naphthalene 1,2-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,87017
Polymers72,6332
Non-polymers1,23715
Water17,493971
1
A: Naphthalene 1,2-dioxygenase subunit alpha
B: Naphthalene 1,2-dioxygenase subunit beta
hetero molecules

A: Naphthalene 1,2-dioxygenase subunit alpha
B: Naphthalene 1,2-dioxygenase subunit beta
hetero molecules

A: Naphthalene 1,2-dioxygenase subunit alpha
B: Naphthalene 1,2-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,61051
Polymers217,9006
Non-polymers3,71045
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 area39060 Å2
ΔGint-256 kcal/mol
Surface area58900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.236, 140.236, 208.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1792-

HOH

21B-1178-

HOH

31B-1306-

HOH

DetailsTHE BIOLOGICAL ASSEMBLY IS AND ALPHA3 BETA3 HEXAMER. ONE ALPHA-BETA DIMER IS IN THE ASSYMETRIC UNIT. THE OTHERS CAN BE GENERATED BY THE THREE-FOLD AXIS: Y, -X-Y, Z -X-Y, X, Z

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Components

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Naphthalene 1,2-dioxygenase subunit ... , 2 types, 2 molecules AB

#1: Protein Naphthalene 1,2-dioxygenase subunit alpha / 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 sp. C18 (bacteria) / Strain: NCIB 9816-4 / Gene: doxB, NC_004999.1 / Plasmid: pDTG121 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STAR / References: UniProt: P0A111, naphthalene 1,2-dioxygenase
#2: Protein Naphthalene 1,2-dioxygenase subunit beta / 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 sp. C18 (bacteria) / Strain: NCIB 9816-4 / Gene: doxD, NC_004999.1 / Plasmid: pDTG121 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STAR / References: UniProt: P0A113, naphthalene 1,2-dioxygenase

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Non-polymers , 6 types, 986 molecules

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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Chemical ChemComp-16R / (methylsulfanyl)benzene / methyl phenyl sulfide


Mass: 124.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 279.15 K / Method: vapor diffusion / pH: 5
Details: 1.9-2.2 M AMMONIUM SULFATE, 4-6%, DIOXANE, 0.1 M MES, pH 5.0, VAPOR DIFFUSION, temperature 279.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.04 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 1, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.3→14.99 Å / Num. obs: 190595 / % possible obs: 99.4 % / Redundancy: 3.99 % / Rmerge(I) obs: 0.083 / Χ2: 1 / Net I/σ(I): 8.1 / Scaling rejects: 5754
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.3-1.352.510.5291.645699181861.1395.6
1.35-1.43.550.5082.167743190221.1699.7
1.4-1.464.110.4552.678525190341.13100
1.46-1.544.130.3773.179421191121.12100
1.54-1.644.180.2983.880270190821.09100
1.64-1.764.240.2234.781414191270.99100
1.76-1.944.240.1586.682256191511.03100
1.94-2.224.320.0941083707191970.9100
2.22-2.84.250.06115.682722192170.8399.8
2.8-14.994.320.03525.685224194670.7699.3

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Processing

Software
NameVersionClassificationNB
d*TREK9.2LDzdata reduction
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→14.988 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8602 / SU ML: 0.17 / σ(F): 0.63 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 9369 5.01 %
Rwork0.1695 --
obs0.1707 190595 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.55 Å2 / Biso mean: 16.8508 Å2 / Biso min: 6.65 Å2
Refinement stepCycle: LAST / Resolution: 1.3→14.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5073 0 65 971 6109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065266
X-RAY DIFFRACTIONf_angle_d1.1737106
X-RAY DIFFRACTIONf_chiral_restr0.079740
X-RAY DIFFRACTIONf_plane_restr0.005927
X-RAY DIFFRACTIONf_dihedral_angle_d13.9781903
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.31480.3485360.348496891022582
1.3148-1.33020.37535380.3477102411077986
1.3302-1.34640.34035830.3357107671135091
1.3464-1.36350.35565620.3144114561201896
1.3635-1.38140.33136330.3117116411227498
1.3814-1.40030.32765720.28821190912481100
1.4003-1.42030.31616650.28431181212477100
1.4203-1.44150.30216470.26931183712484100
1.4415-1.4640.28176550.2581171012365100
1.464-1.4880.28616400.24811189912539100
1.488-1.51360.25736320.22481174612378100
1.5136-1.54110.23956650.21231187312538100
1.5411-1.57070.25395680.20791188612454100
1.5707-1.60270.24316340.19211179012424100
1.6027-1.63750.24386580.17961185912517100
1.6375-1.67560.1945780.171191312491100
1.6756-1.71740.21185730.16191193512508100
1.7174-1.76380.19226460.1591184412490100
1.7638-1.81560.1895800.1561191612496100
1.8156-1.87410.18016340.14431188312517100
1.8741-1.9410.18526050.1487117591236499
1.941-2.01850.1656680.14141178112449100
2.0185-2.11010.1676200.13091187812498100
2.1101-2.2210.16056250.13231191212537100
2.221-2.35970.16865600.1358115561211697
2.3597-2.54110.17616400.13981187212512100
2.5411-2.79530.16766380.14521183612474100
2.7953-3.19640.1726220.151187012492100
3.1964-4.01420.14496630.1382117161237999
4.0142-14.9890.14365900.1475115581214897

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