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- PDB-4hm4: Naphthalene 1,2-Dioxygenase bound to indan -

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Basic information

Entry
Database: PDB / ID: 4hm4
TitleNaphthalene 1,2-Dioxygenase bound to indan
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
2,3-dihydro-1H-indene / : / 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: 1.5 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 1.1Sep 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 1.2Nov 6, 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)73,86417
Polymers72,6332
Non-polymers1,23115
Water12,592699
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)221,59251
Polymers217,9006
Non-polymers3,69245
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 area39000 Å2
ΔGint-251 kcal/mol
Surface area58820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.097, 140.097, 208.222
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-1598-

HOH

21B-1167-

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, 714 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-16N / 2,3-dihydro-1H-indene / indan


Mass: 118.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 54.56 %
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: 1.5→15.95 Å / Num. obs: 124179 / % possible obs: 99.4 % / Redundancy: 6.73 % / Rmerge(I) obs: 0.101 / Χ2: 1 / Net I/σ(I): 10 / Scaling rejects: 6318
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.5-1.554.330.5842.451102117871.1495.1
1.55-1.625.840.4873.272600123761.1599.5
1.62-1.696.910.4213.985765123771.11100
1.69-1.786.950.3484.686819124391.07100
1.78-1.897.030.2765.687866124411.03100
1.89-2.037.080.27.788557124041.06100
2.03-2.247.080.1410.389563124911.01100
2.24-2.567.260.10912.891705124980.8999.9
2.56-3.227.410.08216.393847125620.8399.9
3.22-15.957.280.04826.894514128040.8899.9

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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: 1.5→15.946 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8854 / SU ML: 0.17 / σ(F): 0.71 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1962 6224 5.02 %
Rwork0.1587 --
obs0.1606 124170 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.26 Å2 / Biso mean: 18.6474 Å2 / Biso min: 3.68 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5073 0 66 699 5838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065260
X-RAY DIFFRACTIONf_angle_d1.1567101
X-RAY DIFFRACTIONf_chiral_restr0.077740
X-RAY DIFFRACTIONf_plane_restr0.004926
X-RAY DIFFRACTIONf_dihedral_angle_d13.761905
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 (%)
1.5-1.5170.33143900.29536912730290
1.517-1.53490.32633790.29067086746592
1.5349-1.55360.32193770.27057327770495
1.5536-1.57320.29793400.25297476781696
1.5732-1.59390.28733930.23557653804699
1.5939-1.61570.27374230.214777198142100
1.6157-1.63880.27654100.203777128122100
1.6388-1.66320.26023840.19277268110100
1.6632-1.68920.24544150.182476808095100
1.6892-1.71680.21744230.172277178140100
1.7168-1.74640.21074260.166277488174100
1.7464-1.77810.2194140.162676848098100
1.7781-1.81230.21743500.157877448094100
1.8123-1.84920.20584230.147677098132100
1.8492-1.88940.19214360.142277458181100
1.8894-1.93320.17784070.143976918098100
1.9332-1.98150.1843840.143777288112100
1.9815-2.0350.1843950.135576908085100
2.035-2.09470.17484030.137277658168100
2.0947-2.16220.18713900.133377308120100
2.1622-2.23930.18653740.135277458119100
2.2393-2.32870.17474020.135777198121100
2.3287-2.43430.17784220.136876938115100
2.4343-2.56210.19194090.14277258134100
2.5621-2.72190.18434620.148876648126100
2.7219-2.93090.19014080.161177168124100
2.9309-3.22360.16544100.164677068116100
3.2236-3.68510.18434360.148576958131100
3.6851-4.6240.15824360.139476788114100
4.624-15.9470.19423990.164377268125100

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