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- PDB-2bmq: The Crystal Structure of Nitrobenzene Dioxygenase in complex with... -

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Basic information

Entry
Database: PDB / ID: 2bmq
TitleThe Crystal Structure of Nitrobenzene Dioxygenase in complex with nitrobenzene
Components
  • OXYGENASE-ALPHA NBDO
  • OXYGENASE-BETA NBDO
KeywordsOXIDOREDUCTASE / NITROBENZENE DIOXYGENASE / NITROARENE / RIESKE NON-HEME DIOXYGENASE / SUBSTRATE SPECIFICITY IRON-SULFUR / METAL-BINDING / NAD
Function / homology
Function and homology information


3-phenylpropionate catabolic process / dioxygenase activity / catabolic process / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / 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
ETHANOL / : / FE2/S2 (INORGANIC) CLUSTER / NITROBENZENE / NICKEL (II) ION / Oxygenase-beta NBDO / Oxygenase-alpha NBDO
Similarity search - Component
Biological speciesCOMAMONAS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFriemann, R. / Ivkovic-Jensen, M.M. / Lessner, D.J. / Yu, C. / Gibson, D.T. / Parales, R.E. / Eklund, H. / Ramaswamy, S.
CitationJournal: J. Mol. Biol. / Year: 2005
Title: Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase.
Authors: Friemann, R. / Ivkovic-Jensen, M.M. / Lessner, D.J. / Yu, C.L. / Gibson, D.T. / Parales, R.E. / Eklund, H. / Ramaswamy, S.
History
DepositionMar 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OXYGENASE-ALPHA NBDO
B: OXYGENASE-BETA NBDO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,85819
Polymers72,7372
Non-polymers1,12117
Water12,592699
1
A: OXYGENASE-ALPHA NBDO
B: OXYGENASE-BETA NBDO
hetero molecules

A: OXYGENASE-ALPHA NBDO
B: OXYGENASE-BETA NBDO
hetero molecules

A: OXYGENASE-ALPHA NBDO
B: OXYGENASE-BETA NBDO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,57357
Polymers218,2106
Non-polymers3,36351
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)121.533, 121.533, 84.179
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-2249-

HOH

21B-2297-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein OXYGENASE-ALPHA NBDO / NITROBENZENE DIOXYGENASE


Mass: 49614.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COMAMONAS SP. (bacteria) / Strain: JS765
Description: WASTE TREATMENT PLANT IN NEW JERSEY. (SF NISHINO AND JC SPAIN. 1995. APPL. ENVIRON. MICROBIOL.
Plasmid: PDTG927 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q8RTL4
#2: Protein OXYGENASE-BETA NBDO / NITROBENZENE DIOXYGENASE


Mass: 23122.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) COMAMONAS SP. (bacteria) / Strain: JS765
Description: WASTE TREATMENT PLANT IN NEW JERSEY. (SF NISHINO AND JC SPAIN. 1995. APPL. ENVIRON. MICROBIOL. 61\:2308-2313)
Plasmid: PDTG927 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q8RTL3

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Non-polymers , 7 types, 716 molecules

#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-NBZ / NITROBENZENE


Mass: 123.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O
#8: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#9: 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.26 %
Crystal growDetails: 0.1M HEPES PH 6.5, 6% PEG 8000 (W/V), 5MM NISO4, 50 MM NITROBENZENE. THE NITROBENZENE WAS PREPARED FROM A 1M STOCKSOLUTION WHERE NITROBENZENE WAS DISOLVED IN ETHANOL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.03347
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 22, 2003
RadiationMonochromator: SINGLE ASYMMETRICALLY CUT SI(111) CRYSTAL WITH HORIZONTAL DIFFRACTION PLANE.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03347 Å / Relative weight: 1
ReflectionResolution: 1.55→27.63 Å / Num. obs: 99964 / % possible obs: 98.5 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.7
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BMO

2bmo


Resolution: 1.55→27 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.287 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 5050 5 %RANDOM
Rwork0.167 ---
obs0.169 95726 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.22 Å20 Å2
2---0.44 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.55→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5048 0 58 699 5805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215316
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9317205
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2345668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41323.822259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07315833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6131532
X-RAY DIFFRACTIONr_chiral_restr0.0920.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024191
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.22615
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23670
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2579
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.2149
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.266
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6581.53327
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09525215
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.77932287
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.554.51988
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.27 348
Rwork0.244 7146

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