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- PDB-3en1: Crystal structure of Toluene 2,3-Dioxygenase -

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Basic information

Entry
Database: PDB / ID: 3en1
TitleCrystal structure of Toluene 2,3-Dioxygenase
Components(Benzene 1,2-dioxygenase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Iron-sulfur cluster / mononuclear iron / 2Fe-2S / Aromatic hydrocarbons catabolism / Dioxygenase / Iron / Iron-sulfur / Metal-binding / NAD
Function / homology
Function and homology information


toluene dioxygenase / benzene 1,2-dioxygenase / benzene 1,2-dioxygenase activity / toluene dioxygenase activity / xylene catabolic process / toluene 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] 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 / TOLUENE / Chem-PE3 / Benzene 1,2-dioxygenase subunit beta / Benzene 1,2-dioxygenase subunit alpha / Benzene 1,2-dioxygenase subunit alpha / Benzene 1,2-dioxygenase subunit beta
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsFriemann, R. / Lee, K. / Brown, E.N. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structures of the multicomponent Rieske non-heme iron toluene 2,3-dioxygenase enzyme system
Authors: Friemann, R. / Lee, K. / Brown, E.N. / Gibson, D.T. / Eklund, H. / Ramaswamy, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Purification, crystallization and preliminary X-ray diffraction studies of the three components of the toluene 2,3-dioxygenase enzyme system
Authors: Lee, K. / Friemann, R. / Parales, J.V. / Gibson, D.T. / Ramaswamy, S.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_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: Benzene 1,2-dioxygenase subunit alpha
B: Benzene 1,2-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0607
Polymers73,0462
Non-polymers1,0145
Water32418
1
A: Benzene 1,2-dioxygenase subunit alpha
B: Benzene 1,2-dioxygenase subunit beta
hetero molecules

A: Benzene 1,2-dioxygenase subunit alpha
B: Benzene 1,2-dioxygenase subunit beta
hetero molecules

A: Benzene 1,2-dioxygenase subunit alpha
B: Benzene 1,2-dioxygenase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,18121
Polymers219,1386
Non-polymers3,04315
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
Buried area32080 Å2
ΔGint-75 kcal/mol
Surface area55260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.531, 234.531, 234.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11B-188-

FE2

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Components

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Benzene 1,2-dioxygenase subunit ... , 2 types, 2 molecules AB

#1: Protein Benzene 1,2-dioxygenase subunit alpha / / Benzene 1 / 2-dioxygenase P1 subunit / Toluene 2 / 3-dioxygenase subunit alpha


Mass: 51004.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / Gene: bnzA, TodA, todC1 / Production host: Escherichia coli (E. coli) / Strain (production host): CGSC#7692
References: UniProt: P0C618, UniProt: A5W4F2*PLUS, toluene dioxygenase
#2: Protein Benzene 1,2-dioxygenase subunit beta / / Benzene 1 / 2-dioxygenase P2 subunit / Toluene 2 / 3-dioxygenase subunit beta


Mass: 22041.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / Gene: bnzB, TodB, todC2 / Production host: Escherichia coli (E. coli) / Strain (production host): CGSC#7692
References: UniProt: P0C619, UniProt: A5W4F1*PLUS, toluene dioxygenase

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Non-polymers , 5 types, 23 molecules

#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL / Polyethylene glycol


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#6: Chemical ChemComp-MBN / TOLUENE / Toluene


Mass: 92.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 7.36 Å3/Da
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 40% (w/v) polyethylene glycol 600, 0.1 M sodium citrate pH 6.1, 20 50 mM Fe(NH4)2(SO4)2, 50 mM Toluene, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 26, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.2→165.839 Å / Num. all: 36887 / Num. obs: 36887 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 24 % / Rmerge(I) obs: 0.116 / Rsym value: 0.116 / Net I/σ(I): 6.003
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.2-3.3724.70.381213023452760.381100
3.37-3.5824.60.256312310250090.256100
3.58-3.8224.50.1814.211597647360.181100
3.82-4.1324.40.1295.610746344040.129100
4.13-4.5324.30.17.19916240880.1100
4.53-5.0624.10.0828.38917737030.082100
5.06-5.8423.80.08587873133040.085100
5.84-7.1623.40.0798.46619228330.079100
7.16-10.1222.60.0629.55075922500.062100
10.12-29.7820.20.0599.82591212840.05996.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.372 / Cor.coef. Fo:Fc: 0.647 / Cor.coef. Io to Ic: 0.492
Highest resolutionLowest resolution
Rotation3.2 Å30 Å
Translation3.2 Å30 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.1.20data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ProDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.887 / SU B: 9.504 / SU ML: 0.168 / SU R Cruickshank DPI: 0.343 / SU Rfree: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1836 5 %RANDOM
Rwork0.185 ---
all0.186 ---
obs0.186 36694 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.19 Å2 / Biso mean: 48.958 Å2 / Biso min: 12.42 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 27 18 4917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215017
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9366795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1735601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43123.18261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35315814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8641546
X-RAY DIFFRACTIONr_chiral_restr0.1110.2708
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023922
X-RAY DIFFRACTIONr_nbd_refined0.2210.22259
X-RAY DIFFRACTIONr_nbtor_refined0.3160.23409
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.2140
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.217
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1130.21
X-RAY DIFFRACTIONr_mcbond_it0.7111.53059
X-RAY DIFFRACTIONr_mcangle_it1.27824832
X-RAY DIFFRACTIONr_scbond_it1.56932237
X-RAY DIFFRACTIONr_scangle_it2.714.51963
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 119 -
Rwork0.239 2487 -
all-2606 -
obs--100 %

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