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- PDB-2b1x: Crystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp. -

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Basic information

Entry
Database: PDB / ID: 2b1x
TitleCrystal structure of naphthalene 1,2-dioxygenase from Rhodococcus sp.
Components(naphthalene dioxygenase ...) x 2
KeywordsOXIDOREDUCTASE / RIESKE NON-HEME IRON OXYGENASE
Function / homology
Function and homology information


3-phenylpropionate catabolic process / dioxygenase activity / catabolic process / 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] 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 / 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: 2 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: Advisory / 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_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_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)219,48325
Polymers217,2526
Non-polymers2,23119
Water20,0331112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34770 Å2
ΔGint-357 kcal/mol
Surface area55520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.744, 144.246, 186.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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, 1131 molecules

#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: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1112 / 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: 2.8 Å3/Da / Density % sol: 55.5 %
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: 19-ID / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2001
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→20.8 Å / Num. all: 147609 / Num. obs: 147609 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 7.4
Reflection shellResolution: 2→2.051 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.54 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SBC-Collectdata collection
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NDO

1ndo


Resolution: 2→20.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.053 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.173 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22431 2984 2 %RANDOM
Rwork0.19058 ---
all0.19127 144987 --
obs0.19127 144987 92.77 %-
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: 19.109 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--1.4 Å20 Å2
3----0.21 Å2
Refine analyzeLuzzati coordinate error free: 0.153 Å
Refinement stepCycle: LAST / Resolution: 2→20.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14562 0 119 1112 15793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02115043
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.95120437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64251818
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_restr0.1180.22170
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211670
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.26928
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.21147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.59069
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.303214607
X-RAY DIFFRACTIONr_scbond_it2.20735974
X-RAY DIFFRACTIONr_scangle_it3.4484.55824
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.265 159
Rwork0.255 9119
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.158-0.12270.21220.3842-0.38280.8818-0.03880.06010.0877-0.0076-0.0998-0.1271-0.08950.18690.13860.1011-0.0285-0.00390.09810.08920.161437.15515.99855.789
20.1933-0.1708-0.28780.4538-0.2360.9375-0.0040.04780.11970.12480.01880.0002-0.2693-0.0604-0.01480.19960.0494-0.03190.0170.0190.159814.2826.75874.153
30.14490.1884-0.16460.4225-0.31510.4979-0.0460.08970.0219-0.14910.11640.06990.1433-0.2296-0.07040.1266-0.0747-0.04850.17470.04730.0783-1.729-11.31656.396
40.17350.07070.02520.6094-0.09070.6308-0.01930.01310.08840.05230.0790.0907-0.0898-0.2403-0.05970.05540.05580.01080.15240.04790.1231-4.6948.25980.572
50.3204-0.13250.11160.187-0.19860.5379-0.03560.0170.0543-0.0267-0.009-0.05880.02410.05920.04460.07620.0052-0.00620.02640.0090.059931.548-16.5589.873
60.4146-0.1950.08010.7609-0.29890.5973-0.0828-0.02280.09470.13510.0504-0.0429-0.2145-0.08730.03240.16010.042-0.03020.0371-0.0220.068217.61610.73195.977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4411 - 441
2X-RAY DIFFRACTION2BB513 - 6796 - 172
3X-RAY DIFFRACTION3CC1 - 4411 - 441
4X-RAY DIFFRACTION4DD513 - 6796 - 172
5X-RAY DIFFRACTION5EE1 - 4411 - 441
6X-RAY DIFFRACTION6FF513 - 6796 - 172

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