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- PDB-4p1c: CRYSTAL STRUCTURE OF THE TOLUENE 4-MONOOXYGENASE HYDROXYLASE-FERR... -

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Basic information

Entry
Database: PDB / ID: 4p1c
TitleCRYSTAL STRUCTURE OF THE TOLUENE 4-MONOOXYGENASE HYDROXYLASE-FERREDOXIN C7S, C84A, C85A VARIANT ELECTRON-TRANSFER COMPLEX
Components
  • (Toluene-4-monooxygenase system protein ...) x 3
  • Toluene-4-monooxygenase system ferredoxin subunit
KeywordsOXIDOREDUCTASE / ELECTRON-TRANSFER COMPLEX / DIIRON ENZYME COMPLEX / IRON-SULFUR / REDUCTION / HYDROXYLASE FERREDOXIN / OXYGENASE
Function / homology
Function and homology information


toluene 4-monooxygenase / toluene 4-monooxygenase activity / toluene catabolic process / 2 iron, 2 sulfur cluster binding / 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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Ribonucleotide Reductase, subunit A ...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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / 3-layer Sandwich / Ribonucleotide reductase-like / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Ferritin-like superfamily / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / DI(HYDROXYETHYL)ETHER / Toluene-4-monooxygenase system, hydroxylase component subunit alpha / Toluene-4-monooxygenase system, hydroxylase component subunit gamma / Toluene-4-monooxygenase system, ferredoxin component / Toluene-4-monooxygenase system, hydroxylase component subunit beta
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAcheson, J.F. / Fox, B.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0843239 United States
Department of Energy (DOE, United States)W-31-109-ENG-38 United States
CitationJournal: Nat Commun / Year: 2014
Title: Structural basis for biomolecular recognition in overlapping binding sites in a diiron enzyme system.
Authors: Acheson, J.F. / Bailey, L.J. / Elsen, N.L. / Fox, B.G.
History
DepositionFeb 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references / Derived calculations
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toluene-4-monooxygenase system protein A
B: Toluene-4-monooxygenase system protein E
C: Toluene-4-monooxygenase system protein B
D: Toluene-4-monooxygenase system protein A
E: Toluene-4-monooxygenase system protein E
F: Toluene-4-monooxygenase system protein B
H: Toluene-4-monooxygenase system ferredoxin subunit
I: Toluene-4-monooxygenase system ferredoxin subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,76016
Polymers228,9738
Non-polymers7878
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30500 Å2
ΔGint-247 kcal/mol
Surface area66340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.227, 106.353, 213.418
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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Toluene-4-monooxygenase system protein ... , 3 types, 6 molecules ADBECF

#1: Protein Toluene-4-monooxygenase system protein A / Toluene-4-monooxygenase hydroxylase subunit / T4moH


Mass: 57089.910 Da / Num. of mol.: 2 / Mutation: Stop>492
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoA / Plasmid: PVP58KABE3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q00456, 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
#2: Protein Toluene-4-monooxygenase system protein E / T4moE


Mass: 35930.363 Da / Num. of mol.: 2 / Mutation: STOP>307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoE / Plasmid: PVP58KABE3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q00460, 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
#3: Protein Toluene-4-monooxygenase system protein B / T4moB


Mass: 9340.679 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoB / Plasmid: PVP58KABE3 / 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, 2 molecules HI

#4: Protein Toluene-4-monooxygenase system ferredoxin subunit / Toluene-4-monooxygenase system protein C / T4moC


Mass: 12125.305 Da / Num. of mol.: 2 / Mutation: C7S C84A C85A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Gene: tmoC / Plasmid: PET15BCDTET / Details (production host): C7S C84A C85A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q00458

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Non-polymers , 4 types, 617 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsW336 AND Y227 ARE THE RESIDUES IN STRUCTURE. THERE MAY BE ERRORS IN THE ORIGINAL SEQUENCING OF THE ...W336 AND Y227 ARE THE RESIDUES IN STRUCTURE. THERE MAY BE ERRORS IN THE ORIGINAL SEQUENCING OF THE GENE, AS THESE RESIDUES SEEM STRUCTURALLY SOUND AND GREATLY DIFFER FOR THE UNIPROT RESIDUES.

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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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 MM MOPS/HEPES, 20% PEG 3350, 5% JEFFAMINE 200 MM AMMONIUM CHLORIDE, 10 MM MGCL2, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2011
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→47.69 Å / Num. obs: 81284 / % possible obs: 94.6 % / Observed criterion σ(I): 1.7 / Redundancy: 6 % / Biso Wilson estimate: 27.96 Å2 / Rsym value: 0.129 / Net I/σ(I): 12.4
Reflection shellResolution: 2.4→2.43 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.76 / % possible all: 93

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(PHENIX.REFINE: DEV_1184)refinement
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DHG

3dhg


Resolution: 2.4→47.69 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4093 5.04 %Random selection
Rwork0.153 ---
obs0.156 81284 95.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16126 0 24 609 16759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816637
X-RAY DIFFRACTIONf_angle_d1.07722615
X-RAY DIFFRACTIONf_dihedral_angle_d14.7976034
X-RAY DIFFRACTIONf_chiral_restr0.0772311
X-RAY DIFFRACTIONf_plane_restr0.0052924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42820.23471270.17542625X-RAY DIFFRACTION93
2.4282-2.45790.29991460.19262569X-RAY DIFFRACTION93
2.4579-2.4890.34091250.20842547X-RAY DIFFRACTION93
2.489-2.52170.2971560.20392532X-RAY DIFFRACTION93
2.5217-2.55630.31891230.19092572X-RAY DIFFRACTION93
2.5563-2.59280.25341320.18292621X-RAY DIFFRACTION93
2.5928-2.63150.26781340.17282523X-RAY DIFFRACTION92
2.6315-2.67260.26461350.17732576X-RAY DIFFRACTION93
2.6726-2.71640.27731450.17522540X-RAY DIFFRACTION92
2.7164-2.76320.26321200.17892578X-RAY DIFFRACTION93
2.7632-2.81350.2451550.17712534X-RAY DIFFRACTION92
2.8135-2.86760.26361460.17792564X-RAY DIFFRACTION92
2.8676-2.92610.2461380.1712560X-RAY DIFFRACTION93
2.9261-2.98970.22561260.1712555X-RAY DIFFRACTION92
2.9897-3.05930.22221150.1682578X-RAY DIFFRACTION92
3.0593-3.13580.26031420.17932561X-RAY DIFFRACTION93
3.1358-3.22050.24531400.17182584X-RAY DIFFRACTION93
3.2205-3.31530.22711370.17412614X-RAY DIFFRACTION94
3.3153-3.42220.21461340.16352678X-RAY DIFFRACTION96
3.4222-3.54450.22671320.15272743X-RAY DIFFRACTION97
3.5445-3.68640.1881300.14612742X-RAY DIFFRACTION98
3.6864-3.85410.21631360.13222800X-RAY DIFFRACTION99
3.8541-4.05720.17151640.12682773X-RAY DIFFRACTION100
4.0572-4.31120.18111610.11812820X-RAY DIFFRACTION100
4.3112-4.64380.1441350.11232833X-RAY DIFFRACTION100
4.6438-5.11070.18121550.12412849X-RAY DIFFRACTION100
5.1107-5.84910.19481630.13952845X-RAY DIFFRACTION100
5.8491-7.36490.18921750.15752866X-RAY DIFFRACTION100
7.3649-47.690.1631660.14273009X-RAY DIFFRACTION100

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