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- PDB-5xbp: Oxygenase component of 3-nitrotoluene dioxygenase from Diaphoroba... -

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Basic information

Entry
Database: PDB / ID: 5xbp
TitleOxygenase component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2
Components
  • 3NT oxygenase alpha subunit
  • 3NT oxygenase beta subunit
KeywordsMETAL BINDING PROTEIN / Rieske non-heme oxygenase / iron-sulfur clusters / oxidoreductase / nitroaromatic compounds degrader
Function / homology
Function and homology information


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
: / FE2/S2 (INORGANIC) CLUSTER / 3NT oxygenase beta subunit / 3NT oxygenase alpha subunit
Similarity search - Component
Biological speciesDiaphorobacter sp. DS2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRamaswamy, S. / Kumari, A. / Singh, D. / Gurunath, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of biotechnologyDBT/PR5801/INF/22/156/2012 India
Citation
Journal: PLoS ONE / Year: 2017
Title: Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2.
Authors: Kumari, A. / Singh, D. / Ramaswamy, S. / Ramanathan, G.
#1: Journal: To Be Published
Title: Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2
Authors: Kumari, A. / Ramaswamy, S.
History
DepositionMar 21, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 19, 2017ID: 5BRC
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: 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 / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_conn_type.id
Revision 1.3Oct 30, 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: 3NT oxygenase alpha subunit
C: 3NT oxygenase beta subunit
D: 3NT oxygenase alpha subunit
F: 3NT oxygenase beta subunit
G: 3NT oxygenase alpha subunit
I: 3NT oxygenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,31312
Polymers217,6186
Non-polymers6956
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31430 Å2
ΔGint-188 kcal/mol
Surface area60350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.804, 178.804, 242.323
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 3NT oxygenase alpha subunit


Mass: 49588.383 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Diaphorobacter sp. DS2 (bacteria) / Gene: mntAc / Plasmid: pET21a / Details (production host): pDS21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: M9PW10
#2: Protein 3NT oxygenase beta subunit


Mass: 22951.061 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Diaphorobacter sp. DS2 (bacteria) / Gene: mntAd / Details (production host): pDS21 / Production host: Escherichia coli (E. coli) / References: UniProt: M9PV03
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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: 5.14 Å3/Da / Density % sol: 76.06 % / Description: Red orange hexagonal plated sheet
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium citrate tribasic, 18-20% PEG 3350 / PH range: 7.9-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.9→47.711 Å / Num. obs: 95735 / % possible obs: 96.8 % / Redundancy: 5.2 % / CC1/2: 0.984 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.113 / Net I/σ(I): 7.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.346 / Num. unique obs: 4714 / Rpim(I) all: 1.043 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NDO

1ndo


Resolution: 2.9→47.711 Å / SU ML: 0.52 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 32.92
RfactorNum. reflection% reflection
Rfree0.2839 1919 2.01 %
Rwork0.2406 --
obs0.2415 95623 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→47.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15267 0 15 57 15339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01115675
X-RAY DIFFRACTIONf_angle_d1.30621243
X-RAY DIFFRACTIONf_dihedral_angle_d6.0939222
X-RAY DIFFRACTIONf_chiral_restr0.0692226
X-RAY DIFFRACTIONf_plane_restr0.0082775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97250.41341490.37766635X-RAY DIFFRACTION96
2.9725-3.05290.37671310.35886650X-RAY DIFFRACTION97
3.0529-3.14270.40051390.34226710X-RAY DIFFRACTION97
3.1427-3.24410.39121420.31856661X-RAY DIFFRACTION97
3.2441-3.360.36891260.30066716X-RAY DIFFRACTION97
3.36-3.49450.34571360.29146710X-RAY DIFFRACTION97
3.4945-3.65350.33161440.25546686X-RAY DIFFRACTION97
3.6535-3.8460.31141430.24036690X-RAY DIFFRACTION96
3.846-4.08690.23041300.21896688X-RAY DIFFRACTION96
4.0869-4.40220.23671230.20066670X-RAY DIFFRACTION96
4.4022-4.84490.24291400.18696725X-RAY DIFFRACTION96
4.8449-5.5450.22711390.18826685X-RAY DIFFRACTION95
5.545-6.98260.23531500.19656669X-RAY DIFFRACTION95
6.9826-47.71770.1741270.18256809X-RAY DIFFRACTION93

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