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- PDB-3dhh: Crystal Structure of Resting State Toluene 4-Monoxygenase Hydroxy... -

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Basic information

Entry
Database: PDB / ID: 3dhh
TitleCrystal Structure of Resting State Toluene 4-Monoxygenase Hydroxylase Complexed with Effector Protein
Components
  • (toluene 4-monooxygenase hydroxylase ...) x 3
  • Toluene-4-monooxygenase system effector protein
KeywordsOXIDOREDUCTASE / multicomponent monooxygenase / Aromatic hydrocarbons catabolism / FAD / Flavoprotein / Iron / Monooxygenase
Function / homology
Function and homology information


toluene 4-monooxygenase / toluene 4-monooxygenase activity / toluene catabolic process / monooxygenase activity / metal ion binding
Similarity search - Function
Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane/phenol monooxygenase, hydroxylase component ...Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / TmoB-like / Toluene-4-monooxygenase system B / TmoB-like superfamily / Toluene-4-monooxygenase system protein B (TmoB) / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / 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 / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-BROMOPHENOL / : / Toluene-4-monooxygenase system, hydroxylase component subunit alpha / Toluene-4-monooxygenase system, hydroxylase component subunit gamma / Toluene-4-monooxygenase system, effector component / 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: 1.94 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 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.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.value / _struct_conn.pdbx_dist_value / _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: toluene 4-monooxygenase hydroxylase alpha subunit
B: toluene 4-monooxygenase hydroxylase beta subunit
C: toluene 4-monooxygenase hydroxylase gamma subunit
E: Toluene-4-monooxygenase system effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,25114
Polymers117,7924
Non-polymers1,46010
Water13,799766
1
A: toluene 4-monooxygenase hydroxylase alpha subunit
B: toluene 4-monooxygenase hydroxylase beta subunit
C: toluene 4-monooxygenase hydroxylase gamma subunit
E: Toluene-4-monooxygenase system effector protein
hetero molecules

A: toluene 4-monooxygenase hydroxylase alpha subunit
B: toluene 4-monooxygenase hydroxylase beta subunit
C: toluene 4-monooxygenase hydroxylase gamma subunit
E: Toluene-4-monooxygenase system effector protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,50328
Polymers235,5838
Non-polymers2,91920
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area37060 Å2
ΔGint-203 kcal/mol
Surface area64070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.418, 115.613, 182.403
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-725-

HOH

Detailsbiological unit is a dimer of the tetramer

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Components

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Toluene 4-monooxygenase hydroxylase ... , 3 types, 3 molecules ABC

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


Mass: 58169.344 Da / Num. of mol.: 1
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.: 1
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.: 1
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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Protein , 1 types, 1 molecules E

#4: Protein Toluene-4-monooxygenase system effector protein / Toluene-4-monooxygenase system protein D


Mass: 11629.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoD / Plasmid: p58KABE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q00459, 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 , 6 types, 776 molecules

#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#6: Chemical
ChemComp-BML / 4-BROMOPHENOL


Mass: 173.007 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H5BrO
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: AMMONIUM ACETATE, PEG 3350, BIS-TRIS, pH 6.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 91 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2008
RadiationProtocol: molecular replacement / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 7.3 % / Av σ(I) over netI: 20 / Number: 570915 / Rmerge(I) obs: 0.054 / Χ2: 0.95 / D res high: 1.94 Å / D res low: 100 Å / Num. obs: 77912 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.1810097.710.0360.7157
3.324.1898.910.0490.9047.1
2.93.3299.810.0480.9067.4
2.632.999.910.0641.0057.5
2.442.6310010.070.9987.5
2.32.4410010.0770.8897.5
2.182.310010.090.9877.6
2.092.1810010.1141.0077.5
2.012.0910010.1541.0127.5
1.942.0110010.2031.0736.6
ReflectionResolution: 1.94→100 Å / Num. obs: 77912 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.054 / Χ2: 0.949
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.94-2.016.60.20377541.0731100
2.01-2.097.50.15477121.0121100
2.09-2.187.50.11477831.0071100
2.18-2.37.60.0977390.9871100
2.3-2.447.50.07777810.8891100
2.44-2.637.50.0777880.9981100
2.63-2.97.50.06477771.005199.9
2.9-3.327.40.04878170.906199.8
3.32-4.187.10.04978140.904198.9
4.18-10070.03679470.715197.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.431 / Cor.coef. Fo:Fc: 0.56
Highest resolutionLowest resolution
Rotation3 Å57.55 Å
Translation3 Å57.55 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: 1.94→91.29 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.879 / SU B: 2.977 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3889 5 %RANDOM
Rwork0.157 ---
obs0.159 77871 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.58 Å2 / Biso mean: 25.49 Å2 / Biso min: 10.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.73 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.94→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8035 0 65 766 8866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0218441
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.93811480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71751016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35424.099444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.407151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4151557
X-RAY DIFFRACTIONr_chiral_restr0.1040.21181
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026620
X-RAY DIFFRACTIONr_nbd_refined0.2070.24347
X-RAY DIFFRACTIONr_nbtor_refined0.3060.25773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2748
X-RAY DIFFRACTIONr_metal_ion_refined0.0450.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.226
X-RAY DIFFRACTIONr_mcbond_it0.9251.55136
X-RAY DIFFRACTIONr_mcangle_it1.45528028
X-RAY DIFFRACTIONr_scbond_it2.3433925
X-RAY DIFFRACTIONr_scangle_it3.5664.53434
LS refinement shellResolution: 1.942→1.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 268 -
Rwork0.18 5306 -
all-5574 -
obs--97.48 %

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