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- PDB-4hm2: Naphthalene 1,2-Dioxygenase bound to ethylphenylsulfide -

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Basic information

Entry
Database: PDB / ID: 4hm2
TitleNaphthalene 1,2-Dioxygenase bound to ethylphenylsulfide
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 / dioxygenase activity / catabolic process / 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
(ethylsulfanyl)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: 1.6 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 1.1Feb 10, 2021Group: Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.pdbx_synonyms / _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 1.2Sep 18, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
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
Revision 1.3Oct 16, 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)73,88417
Polymers72,6332
Non-polymers1,25115
Water16,484915
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)221,65251
Polymers217,9006
Non-polymers3,75245
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 area39120 Å2
ΔGint-243 kcal/mol
Surface area59110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.036, 140.036, 208.288
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-1297-

HOH

21B-1137-

HOH

31B-1360-

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, 930 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-16M / (ethylsulfanyl)benzene / ethy lphenyl sulfide


Mass: 138.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 915 / 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: 54.54 %
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: 1.26→49.3 Å / Num. obs: 150873 / % possible obs: 72.5 % / Redundancy: 3.02 % / Rmerge(I) obs: 0.064 / Χ2: 0.96 / Net I/σ(I): 10.6 / Scaling rejects: 3443
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.26-1.311.070.5031151714141.176.8
1.31-1.361.210.5051.2705458391.1728.2
1.36-1.421.440.4611.414862103461.0450
1.42-1.51.830.4051.925648140321.0567.7
1.5-1.592.480.3762.943444174881.184.3
1.59-1.723.410.294.466266193011.0993.2
1.72-1.893.450.189669722200311.0396.3
1.89-2.163.540.1059.574286207500.9499.6
2.16-2.723.680.06914.377458208640.8699.7
2.72-49.33.750.03427.278744207720.8497.5

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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: 1.6→47.848 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9042 / SU ML: 0.15 / σ(F): 0.15 / Phase error: 17.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 8865 5.06 %
Rwork0.143 --
obs0.1451 150679 87.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.12 Å2 / Biso mean: 18.4864 Å2 / Biso min: 3.44 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5073 0 66 915 6054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065286
X-RAY DIFFRACTIONf_angle_d1.1287128
X-RAY DIFFRACTIONf_chiral_restr0.078740
X-RAY DIFFRACTIONf_plane_restr0.004929
X-RAY DIFFRACTIONf_dihedral_angle_d14.4911909
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 (%)
1.6-1.61820.25312970.20385244554182
1.6182-1.63720.2573470.20125298564584
1.6372-1.65720.25332820.18855317559984
1.6572-1.67820.22912800.18185391567185
1.6782-1.70030.24243110.18375395570685
1.7003-1.72350.24073310.17055363569485
1.7235-1.74820.24142990.16495387568685
1.7482-1.77430.22152860.16415459574585
1.7743-1.8020.23143020.16095446574886
1.802-1.83150.2252980.15425549584787
1.8315-1.86310.20642750.14295571584687
1.8631-1.8970.17932840.13215595587988
1.897-1.93350.18742860.1365581586788
1.9335-1.9730.17732900.13855677596788
1.973-2.01590.1932690.13355621589089
2.0159-2.06270.19523460.12855638598489
2.0627-2.11430.17912700.12725667593789
2.1143-2.17150.17123040.12245677598189
2.1715-2.23540.18042850.12885660594589
2.2354-2.30750.18372750.12985617589288
2.3075-2.390.17773050.135672597789
2.39-2.48570.20023170.13215613593089
2.4857-2.59880.18792640.13535684594888
2.5988-2.73580.17072750.14025641591688
2.7358-2.90720.17263000.14155609590988
2.9072-3.13160.19962900.14375662595288
3.1316-3.44670.16913050.14035577588288
3.4467-3.94530.16672970.13145572586988
3.9453-4.96980.14033060.12975551585788
4.9698-47.86920.18652890.17715454574385

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