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- PDB-4hkv: Naphthalene 1,2-Dioxygenase bound to benzamide -

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Basic information

Entry
Database: PDB / ID: 4hkv
TitleNaphthalene 1,2-Dioxygenase bound to benzamide
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
: / FE2/S2 (INORGANIC) CLUSTER / BENZAMIDE / 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: 1.65 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 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Sep 18, 2024Group: Database references / Category: citation / citation_author
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

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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)73,86717
Polymers72,6332
Non-polymers1,23415
Water18,8801048
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)221,60151
Polymers217,9006
Non-polymers3,70145
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 area38850 Å2
ΔGint-261 kcal/mol
Surface area59050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.102, 140.102, 208.495
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-1751-

HOH

21B-1183-

HOH

31B-1319-

HOH

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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, 1063 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-UNU / BENZAMIDE


Mass: 121.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1048 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
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: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 1, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→47.89 Å / Num. obs: 94230 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.54 % / Rmerge(I) obs: 0.104 / Χ2: 0.91 / Net I/σ(I): 9.4 / Scaling rejects: 42349
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.65-1.719.090.5372.59152793421.32100
1.71-1.789.270.46939275393581.21100
1.78-1.869.430.3973.69366293481.13100
1.86-1.969.50.3054.89416893591.04100
1.96-2.089.590.2436.19435593670.94100
2.08-2.249.590.1887.79432394040.87100
2.24-2.469.620.1399.69435994100.78100
2.46-2.829.810.098129556194440.69100
2.82-3.559.970.06517.79657494940.62100
3.55-47.899.480.05125.49379197040.6399.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.1Ldata reduction
REFMACrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
d*TREKdata scaling
AMoREphasing
PHENIX1.8_1069refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→47.89 Å / Occupancy max: 1 / Occupancy min: 0.26 / SU ML: 0.15 / σ(F): 0.17 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 4663 5.01 %
Rwork0.166 --
obs0.1678 93053 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.99 Å2 / Biso mean: 23.1107 Å2 / Biso min: 10.24 Å2
Refinement stepCycle: LAST / Resolution: 1.65→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5073 0 66 1048 6187

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