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- PDB-6vk5: Crystal Structure of Methylosinus trichosporium OB3b Soluble Meth... -

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Basic information

Entry
Database: PDB / ID: 6vk5
TitleCrystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex
Components
  • (Methane monooxygenase ...) x 2
  • (Methane monooxygenase) x 2
KeywordsOXIDOREDUCTASE / Methane Monooxygenase Hydroxylase
Function / homology
Function and homology information


methane metabolic process / methane monooxygenase (soluble) / methane monooxygenase [NAD(P)H] activity / 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 / one-carbon metabolic process / monooxygenase activity / metal ion binding
Similarity search - Function
: / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / : / : ...: / Monooxygenase component MmoB/DmpM / Monooxygenase component MmoB/DmpM superfamily / MmoB/DmpM family / Methane monooxygenase, gamma chain / Methane monooxygenase, gamma chain, domain 1 / Methane monooxygenase, gamma chain, domain 2 / Methane monooxygenase, gamma chain superfamily / : / : / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase / Methane/Phenol/Alkene Hydroxylase / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
BENZOIC ACID / : / Methane monooxygenase / Methane monooxygenase regulatory protein B / Methane monooxygenase component A alpha chain / Methane monooxygenase / Methane monooxygenase component A alpha chain / Methane monooxygenase regulatory protein B
Similarity search - Component
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsJones, J.C. / Banerjee, R. / Shi, K. / Aihara, H. / Lipscomb, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118030, GM08347 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118000, GM118047 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Studies of theMethylosinus trichosporiumOB3b Soluble Methane Monooxygenase Hydroxylase and Regulatory Component Complex Reveal a Transient Substrate Tunnel.
Authors: Jones, J.C. / Banerjee, R. / Shi, K. / Aihara, H. / Lipscomb, J.D.
History
DepositionJan 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methane monooxygenase component A alpha chain
B: Methane monooxygenase
C: Methane monooxygenase
D: Methane monooxygenase regulatory protein B
E: Methane monooxygenase component A alpha chain
F: Methane monooxygenase
G: Methane monooxygenase
H: Methane monooxygenase regulatory protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,70145
Polymers279,3368
Non-polymers2,36537
Water25,4731414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62070 Å2
ΔGint-167 kcal/mol
Surface area66120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.615, 105.459, 299.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPGLYGLY(chain 'A' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))AA12 - 31412 - 314
121TRPTRPPHEPHE(chain 'A' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))AA317 - 526317 - 526
211ASPASPGLYGLY(chain 'E' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))EE12 - 31412 - 314
221TRPTRPPHEPHE(chain 'E' and (resid 12 through 315 or resid 317 through 526 or resid 801 through 802))EE317 - 526317 - 526
112PROPROASPASP(chain 'B' and (resid 4 through 212 or resid 214 through 320 or resid 322 through 395))BB4 - 2114 - 211
122THRTHRLEULEU(chain 'B' and (resid 4 through 212 or resid 214 through 320 or resid 322 through 395))BB214 - 320214 - 320
132ALAALAASNASN(chain 'B' and (resid 4 through 212 or resid 214 through 320 or resid 322 through 395))BB322 - 395322 - 395
212PROPROASPASP(chain 'F' and (resid 4 through 212 or resid 214 through 320 or resid 322 through 395))FF4 - 2114 - 211
222THRTHRLEULEU(chain 'F' and (resid 4 through 212 or resid 214 through 320 or resid 322 through 395))FF214 - 320214 - 320
232ALAALAASNASN(chain 'F' and (resid 4 through 212 or resid 214 through 320 or resid 322 through 395))FF322 - 395322 - 395
113ALAALAGLNGLNchain 'C'CC2 - 1682 - 168
213ALAALAGLNGLNchain 'G'GG2 - 1682 - 168
114SERSERARGARGchain 'D'DD2 - 1332 - 133
214SERSERARGARG(chain 'H' and resid 2 through 133)HH2 - 1332 - 133

NCS ensembles :
ID
1
2
3
4

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Components

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Methane monooxygenase ... , 2 types, 4 molecules AEDH

#1: Protein Methane monooxygenase component A alpha chain


Mass: 60031.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D5X0, UniProt: P27353*PLUS
#4: Protein Methane monooxygenase regulatory protein B


Mass: 14896.885 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D0T8, UniProt: P27356*PLUS

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Protein , 2 types, 4 molecules BFCG

#2: Protein Methane monooxygenase


Mass: 45295.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D5X7
#3: Protein Methane monooxygenase


Mass: 19444.400 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D0T0

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Non-polymers , 5 types, 1451 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1414 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tacsimate, 20% w/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.86→105.46 Å / Num. obs: 271196 / % possible obs: 99.8 % / Redundancy: 5 % / Biso Wilson estimate: 28.14 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.132 / Net I/σ(I): 8.2
Reflection shellResolution: 1.86→1.89 Å / Num. unique obs: 13328 / Rpim(I) all: 0.816 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHASERphasing
PHENIXdata processing
PHENIXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MHY, 2MOB

1mhy

2mob


Resolution: 1.86→73.54 Å / SU ML: 0.204 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.002
RfactorNum. reflection% reflection
Rfree0.1931 13530 4.99 %
Rwork0.1699 --
obs0.1711 270925 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.63 Å2
Refinement stepCycle: LAST / Resolution: 1.86→73.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19486 0 143 1414 21043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007320149
X-RAY DIFFRACTIONf_angle_d0.856727299
X-RAY DIFFRACTIONf_chiral_restr0.05022860
X-RAY DIFFRACTIONf_plane_restr0.00583521
X-RAY DIFFRACTIONf_dihedral_angle_d16.07117225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.880.31734130.30438504X-RAY DIFFRACTION99.15
1.88-1.90.31844450.29438436X-RAY DIFFRACTION99.31
1.9-1.930.30224780.29128422X-RAY DIFFRACTION99.32
1.93-1.950.28944580.27368513X-RAY DIFFRACTION99.66
1.95-1.980.284710.25358462X-RAY DIFFRACTION99.68
1.98-20.28124580.24918482X-RAY DIFFRACTION99.72
2-2.030.25794370.23548553X-RAY DIFFRACTION99.76
2.03-2.060.24464280.23338547X-RAY DIFFRACTION99.72
2.06-2.090.25754620.2318480X-RAY DIFFRACTION99.29
2.09-2.130.2394590.21648471X-RAY DIFFRACTION99.6
2.13-2.170.22535030.20228487X-RAY DIFFRACTION99.79
2.17-2.210.23264360.19368535X-RAY DIFFRACTION99.84
2.21-2.250.21794290.1858597X-RAY DIFFRACTION99.83
2.25-2.290.2294310.1888571X-RAY DIFFRACTION99.81
2.29-2.340.19474660.17118531X-RAY DIFFRACTION99.84
2.34-2.40.19544440.16038561X-RAY DIFFRACTION99.84
2.4-2.460.19094790.16288550X-RAY DIFFRACTION99.82
2.46-2.520.18874630.16038514X-RAY DIFFRACTION99.87
2.52-2.60.18894630.15938548X-RAY DIFFRACTION99.87
2.6-2.680.18244210.16078651X-RAY DIFFRACTION99.85
2.68-2.780.18834340.16518659X-RAY DIFFRACTION99.82
2.78-2.890.19254420.16048546X-RAY DIFFRACTION99.84
2.89-3.020.20114000.16728615X-RAY DIFFRACTION99.08
3.02-3.180.19964900.17028557X-RAY DIFFRACTION99.55
3.18-3.380.20654620.17278601X-RAY DIFFRACTION99.79
3.38-3.640.19444350.1638702X-RAY DIFFRACTION99.83
3.64-4.010.15724490.14248677X-RAY DIFFRACTION99.71
4.01-4.590.13264860.12798715X-RAY DIFFRACTION99.6
4.59-5.780.13714760.12738742X-RAY DIFFRACTION99.41
5.78-73.540.18454120.16049166X-RAY DIFFRACTION99.48

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