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- PDB-3dhg: Crystal Structure of Toluene 4-Monoxygenase Hydroxylase -

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Basic information

Entry
Database: PDB / ID: 3dhg
TitleCrystal Structure of Toluene 4-Monoxygenase Hydroxylase
Components(toluene 4-monooxygenase hydroxylase ...) x 3
KeywordsOXIDOREDUCTASE / multicomponent monooxygenase / Aromatic hydrocarbons catabolism / FAD / Flavoprotein / Iron / Monooxygenase
Function / homology
Function and homology information


toluene 4-monooxygenase / toluene catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / monooxygenase activity / metal ion binding
Similarity search - Function
TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like ...TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / : / Toluene-4-monooxygenase system, hydroxylase component subunit alpha / Toluene-4-monooxygenase system, hydroxylase component subunit gamma / Toluene-4-monooxygenase system, hydroxylase component subunit beta / Toluene-4-monooxygenase system, hydroxylase component subunit beta / Toluene-4-monooxygenase system, hydroxylase component subunit alpha
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsBailey, L.J. / Mccoy, J.G. / Phillips Jr., G.N. / Fox, B.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Structural consequences of effector protein complex formation in a diiron hydroxylase.
Authors: Bailey, L.J. / McCoy, J.G. / Phillips Jr., G.N. / Fox, B.G.
History
DepositionJun 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 30, 2013Group: Structure summary
Revision 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Revision 1.5Feb 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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: toluene 4-monooxygenase hydroxylase alpha subunit
B: toluene 4-monooxygenase hydroxylase beta subunit
C: toluene 4-monooxygenase hydroxylase gamma subunit
D: toluene 4-monooxygenase hydroxylase alpha subunit
E: toluene 4-monooxygenase hydroxylase beta subunit
F: toluene 4-monooxygenase hydroxylase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,95120
Polymers212,3256
Non-polymers62614
Water26,2841459
1
A: toluene 4-monooxygenase hydroxylase alpha subunit
B: toluene 4-monooxygenase hydroxylase beta subunit
C: toluene 4-monooxygenase hydroxylase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,51511
Polymers106,1633
Non-polymers3528
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-129 kcal/mol
Surface area30440 Å2
MethodPISA
2
D: toluene 4-monooxygenase hydroxylase alpha subunit
E: toluene 4-monooxygenase hydroxylase beta subunit
F: toluene 4-monooxygenase hydroxylase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4379
Polymers106,1633
Non-polymers2746
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-139 kcal/mol
Surface area30320 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.822, 181.481, 89.917
Angle α, β, γ (deg.)90.000, 107.620, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asymmetric unit

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Components

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Toluene 4-monooxygenase hydroxylase ... , 3 types, 6 molecules ADBECF

#1: Protein toluene 4-monooxygenase hydroxylase alpha subunit / Alpha hydroxylase


Mass: 58169.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoA / Plasmid: p58KABE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6Q8Q7, UniProt: Q00456*PLUS
#2: Protein toluene 4-monooxygenase hydroxylase beta subunit / Beta hydroxylase


Mass: 38392.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoE / Plasmid: p58KABE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6Q8Q3, UniProt: Q00460*PLUS
#3: Protein toluene 4-monooxygenase hydroxylase gamma subunit / Toluene-4-monooxygenase system protein B


Mass: 9600.989 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoB / Plasmid: p58KABE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q00457, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor

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Non-polymers , 4 types, 1473 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1459 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: MEPEG 2K, CaCl2, HEPES, AZIDE, pH 7.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 91 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9273 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2007
RadiationProtocol: molecular replacement / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9273 Å / Relative weight: 1
ReflectionRedundancy: 4.3 % / Av σ(I) over netI: 8.8 / Number: 622080 / Rmerge(I) obs: 0.097 / Χ2: 1.01 / D res high: 1.85 Å / D res low: 100 Å / Num. obs: 145120 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.9910099.710.0430.9124.6
3.163.9999.410.0660.9544.4
2.763.1699.510.0871.0584.4
2.512.7699.710.130.994.5
2.332.5199.910.1821.0514.6
2.192.3310010.2321.0614.6
2.082.1910010.2991.0214.5
1.992.0899.910.381.0454.2
1.921.9997.910.4751.0333.8
1.851.929010.55713.3
ReflectionResolution: 1.85→100 Å / Num. obs: 145120 / % possible obs: 98.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.097 / Χ2: 1.012
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.923.30.557132141190
1.92-1.993.80.475143521.033197.9
1.99-2.084.20.38146641.045199.9
2.08-2.194.50.299147201.0211100
2.19-2.334.60.232146621.0611100
2.33-2.514.60.182146991.051199.9
2.51-2.764.50.13146620.99199.7
2.76-3.164.40.087146911.058199.5
3.16-3.994.40.066146350.954199.4
3.99-1004.60.043148210.912199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.421 / Cor.coef. Fo:Fc: 0.539
Highest resolutionLowest resolution
Rotation3 Å49.42 Å
Translation3 Å49.42 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→49.45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.864 / SU B: 3.19 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 7264 5 %RANDOM
Rwork0.164 ---
obs0.167 145056 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 max: 64.99 Å2 / Biso mean: 24.729 Å2 / Biso min: 10.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.18 Å2
2---0.12 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14424 0 16 1459 15899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02115030
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.92620450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.83151801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14523.909793
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.401152496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5415101
X-RAY DIFFRACTIONr_chiral_restr0.1370.22085
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211801
X-RAY DIFFRACTIONr_nbd_refined0.2080.28117
X-RAY DIFFRACTIONr_nbtor_refined0.3070.210238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.21397
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.245
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0980.21
X-RAY DIFFRACTIONr_mcbond_it0.9441.59117
X-RAY DIFFRACTIONr_mcangle_it1.411214289
X-RAY DIFFRACTIONr_scbond_it2.3237015
X-RAY DIFFRACTIONr_scangle_it3.4444.56137
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 454 -
Rwork0.244 9064 -
all-9518 -
obs--87.38 %

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