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- PDB-3dhi: Crystal Structure of Reduced Toluene 4-Monoxygenase Hydroxylase C... -

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Basic information

Entry
Database: PDB / ID: 3dhi
TitleCrystal Structure of Reduced 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
ACETATE ION / : / 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 / Resolution: 1.68 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: Derived calculations / Version format compliance
Revision 1.2Jan 30, 2013Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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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)118,64810
Polymers117,7924
Non-polymers8576
Water16,736929
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)237,29620
Polymers235,5838
Non-polymers1,71312
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area29330 Å2
ΔGint-195 kcal/mol
Surface area71680 Å2
2
E: Toluene-4-monooxygenase system effector protein

E: Toluene-4-monooxygenase system effector protein

A: toluene 4-monooxygenase hydroxylase alpha subunit
B: toluene 4-monooxygenase hydroxylase beta subunit
C: toluene 4-monooxygenase hydroxylase gamma subunit
hetero molecules

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)237,29620
Polymers235,5838
Non-polymers1,71312
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation5_455x-1/2,y+1/2,z1
crystal symmetry operation8_435x-1/2,-y-3/2,-z1
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area29330 Å2
ΔGint-195 kcal/mol
Surface area71680 Å2
MethodPISA
3
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)237,29620
Polymers235,5838
Non-polymers1,71312
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area37370 Å2
ΔGint-224 kcal/mol
Surface area63640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.661, 115.295, 180.823
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-635-

HOH

Detailsbiological unit is a dimer of 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 , 5 types, 935 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: 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
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 929 / 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: 2.16 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: AMMONIUM ACETATE, PEG 3350, BIS-TRIS, reduced with dithionite in anaerobic conditions, pH 6.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 91 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionRedundancy: 6.6 % / Av σ(I) over netI: 14.3 / Number: 764468 / Rmerge(I) obs: 0.059 / Χ2: 0.97 / D res high: 1.68 Å / D res low: 50 Å / Num. obs: 115518 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.625099.310.0320.6266.4
2.873.6299.810.0530.9556.6
2.512.8710010.0630.9656.7
2.282.5110010.0841.0696.8
2.122.2810010.1011.036.9
1.992.1210010.1210.9276.9
1.891.9910010.1521.0186.9
1.811.8910010.21.0486.9
1.741.8110010.2631.0276.7
1.681.7499.310.3090.9935.4
ReflectionResolution: 1.68→50 Å / Num. obs: 115518 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.059 / Χ2: 0.967
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.68-1.745.40.309113150.993199.3
1.74-1.816.70.263115131.0271100
1.81-1.896.90.2114741.0481100
1.89-1.996.90.152115131.0181100
1.99-2.126.90.121114720.9271100
2.12-2.286.90.101115571.031100
2.28-2.516.80.084115611.0691100
2.51-2.876.70.063115800.9651100
2.87-3.626.60.053116380.955199.8
3.62-506.40.032118950.626199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.68→48.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.877 / SU B: 1.848 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 5782 5 %RANDOM
Rwork0.167 ---
obs0.169 115459 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.46 Å2 / Biso mean: 22.628 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2--0.39 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.68→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8095 0 52 929 9076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228515
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.93711576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46651029
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92824.022445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.314151428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4491558
X-RAY DIFFRACTIONr_chiral_restr0.0950.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026651
X-RAY DIFFRACTIONr_nbd_refined0.2060.24517
X-RAY DIFFRACTIONr_nbtor_refined0.3090.25851
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2802
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.246
X-RAY DIFFRACTIONr_mcbond_it0.7981.55159
X-RAY DIFFRACTIONr_mcangle_it1.25628118
X-RAY DIFFRACTIONr_scbond_it2.01433914
X-RAY DIFFRACTIONr_scangle_it3.1214.53439
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 417 -
Rwork0.221 7844 -
all-8261 -
obs--97.83 %

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