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- PDB-2b24: Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus... -

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Basic information

Entry
Database: PDB / ID: 2b24
TitleCrystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp. bound to indole
Components(naphthalene dioxygenase ...) x 2
KeywordsOXIDOREDUCTASE / RIESKE NON-HEME IRON OXYGENASE
Function / homology
Function and homology information


: / : / dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Ring-hydroxylating dioxygenase large subunit NdoB-related protein, N-terminal Rieske domain / 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 ...Ring-hydroxylating dioxygenase large subunit NdoB-related protein, N-terminal Rieske domain / 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] iron-sulphur domain / Rieske [2Fe-2S] 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 / INDOLE / Aromatic-ring-hydroxylating dioxygenase subunit beta / Iron-sulfur protein / Aromatic ring-hydroxylating dioxygenase subunit alpha
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGakhar, L. / Malik, Z.A. / Allen, C.C. / Lipscomb, D.A. / Larkin, M.J. / Ramaswamy, S.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Structure and Increased Thermostability of Rhodococcus sp. Naphthalene 1,2-Dioxygenase.
Authors: Gakhar, L. / Malik, Z.A. / Allen, C.C. / Lipscomb, D.A. / Larkin, M.J. / Ramaswamy, S.
History
DepositionSep 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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_asym_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_asym_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: naphthalene dioxygenase large subunit
B: naphthalene dioxygenase small subunit
C: naphthalene dioxygenase large subunit
D: naphthalene dioxygenase small subunit
E: naphthalene dioxygenase large subunit
F: naphthalene dioxygenase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,29815
Polymers217,2526
Non-polymers1,0469
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31340 Å2
ΔGint-178 kcal/mol
Surface area55520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.358, 179.358, 245.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12B
22D
32F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPROAA1 - 4401 - 440
21METMETPROPROCC1 - 4401 - 440
31METMETPROPROEE1 - 4401 - 440
12SERSERMETMETBB515 - 6798 - 172
22SERSERMETMETDD515 - 6798 - 172
32SERSERMETMETFF515 - 6798 - 172

NCS ensembles :
ID
1
2

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Components

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Naphthalene dioxygenase ... , 2 types, 6 molecules ACEBDF

#1: Protein naphthalene dioxygenase large subunit


Mass: 52580.902 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodococcus sp. (bacteria) / Strain: NCIMB12038 / References: UniProt: Q9X3R9, naphthalene 1,2-dioxygenase
#2: Protein naphthalene dioxygenase small subunit


Mass: 19836.371 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodococcus sp. (bacteria) / Strain: NCIMB12038
References: UniProt: Q9WVZ0, UniProt: Q7BSK6*PLUS, naphthalene 1,2-dioxygenase

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Non-polymers , 4 types, 321 molecules

#3: Chemical ChemComp-FE / FE (III) ION / Iron


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


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-IND / INDOLE / Indole


Mass: 117.148 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H7N
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 4.54 Å3/Da / Density % sol: 72.91 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M HEPES, PH 7.8, 68% MPD, 40 MG/ML PROTEIN, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2002
RadiationMonochromator: CRYOGENICALLY COOLED SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20.42 Å / Num. all: 79677 / Num. obs: 79677 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.3
Reflection shellResolution: 3→3.11 Å / Redundancy: 4.16 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 5.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
d*TREKdata reduction
d*TREKdata scaling
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B1X

2b1x


Resolution: 3→20.42 Å / Cor.coef. Fo:Fc: 0.84 / Cor.coef. Fo:Fc free: 0.827 / SU B: 26.942 / SU ML: 0.519 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.802 / ESU R Free: 0.4 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29992 2397 3 %RANDOM
Rwork0.28688 ---
all0.28728 77193 --
obs0.28728 77193 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 92.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.8 Å20 Å2
3----1.6 Å2
Refine analyzeLuzzati coordinate error free: 0.4 Å
Refinement stepCycle: LAST / Resolution: 3→20.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14508 0 42 312 14862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02114922
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.94620256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41551806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.22142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211649
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.26853
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2540
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2350.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5871.59018
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1214526
X-RAY DIFFRACTIONr_scbond_it1.09935904
X-RAY DIFFRACTIONr_scangle_it1.9194.55724
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3519tight positional0.040.05
12C3519tight positional0.040.05
13E3519tight positional0.040.05
21B1330tight positional0.040.05
22D1330tight positional0.040.05
23F1330tight positional0.040.05
11A3519tight thermal0.080.5
12C3519tight thermal0.10.5
13E3519tight thermal0.090.5
21B1330tight thermal0.070.5
22D1330tight thermal0.080.5
23F1330tight thermal0.080.5
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.421 162
Rwork0.44 5483

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