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- PDB-7m8r: Complex structure of Methane monooxygenase hydroxylase and regula... -

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Basic information

Entry
Database: PDB / ID: 7m8r
TitleComplex structure of Methane monooxygenase hydroxylase and regulatory subunit with fluorosubstituted tryptophans
Components(Methane monooxygenase ...) x 4
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


methane monooxygenase activity / methane metabolic 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
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 / Methane monooxygenase, hydrolase gamma chain / Methane/phenol monooxygenase, hydroxylase component / Propane/methane/phenol/toluene hydroxylase ...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 / : / 1,1,1-tris(fluoranyl)propan-2-one / Methane monooxygenase / Methane monooxygenase regulatory protein B / Methane monooxygenase component A alpha chain / Methane monooxygenase
Similarity search - Component
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.22 Å
AuthorsJohns, J.C. / Banerjee, R. / Shi, K. / Semonis, M.M. / Aihara, H. / Pomerantz, W.C.K. / Lipscomb, J.D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118030 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM08347 United States
CitationJournal: Biochemistry / Year: 2021
Title: Soluble Methane Monooxygenase Component Interactions Monitored by 19 F NMR.
Authors: Jones, J.C. / Banerjee, R. / Shi, K. / Semonis, M.M. / Aihara, H. / Pomerantz, W.C.K. / Lipscomb, J.D.
History
DepositionMar 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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


Theoretical massNumber of molelcules
Total (without water)278,92955
Polymers275,8438
Non-polymers3,08647
Water31,7781764
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.388, 105.466, 298.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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-IDDetails
12NULL
22NULL
13NULL
23NULL
14NULL
24NULL

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth seq-ID
112NULL0
212NULL0
113NULL0
213NULL0
114NULL0
214NULL0

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.0462770044084, 0.998795090138, 0.0163342211121), (0.998788104608, 0.0459900249739, 0.0175282542571), (0.0167559230538, 0.0171255808443, -0.999712935559)-25.4083296198, 23.0674355113, 74.074235983
2given(-0.0459526023685, 0.998795324, 0.0172121785647), (0.99882317927, 0.0456726845976, 0.0163175499067), (0.0155117661432, 0.0179417567986, -0.999718699672)-25.4252386183, 23.0907489678, 74.0922512093
3given(-0.0435318107558, 0.998908793309, 0.0169175678539), (0.99889276115, 0.0432162626206, 0.0185904913039), (0.0178390911801, 0.0177081138148, -0.999684044852)-25.4487413944, 23.1336362245, 74.0527341114
4given(-0.0433439465759, 0.998907463909, 0.0174694259257), (0.998937167686, 0.0430575602508, 0.0164493623219), (0.0156791999405, 0.018163839137, -0.999712077369)-25.5982310174, 23.1841765021, 74.0650817155

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Components

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Methane monooxygenase ... , 4 types, 8 molecules AEBFCGDH

#1: Protein Methane monooxygenase component A alpha chain /


Mass: 58971.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_12480 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D2D5X0
#2: Protein Methane monooxygenase beta chain


Mass: 44948.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_12475 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D2D5X7
#3: Protein Methane monooxygenase gamma chain


Mass: 19313.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_12465 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D2D0T0
#4: Protein Methane monooxygenase regulatory protein B


Mass: 14688.556 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: CQW49_12470 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D2D0T8

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Non-polymers , 6 types, 1811 molecules

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


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


Mass: 62.068 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#8: Chemical ChemComp-W6X / 1,1,1-tris(fluoranyl)propan-2-one / Trifluoroacetone


Mass: 112.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H3F3O
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1764 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: TACSIMATE AND 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: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.22→149.09 Å / Num. obs: 158676 / % possible obs: 99 % / Redundancy: 5.1 % / Biso Wilson estimate: 37.37 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 8.9
Reflection shellResolution: 2.22→2.25 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.05 / Num. unique obs: 4778 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6VK5

6vk5


Resolution: 2.22→86.1 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 7787 4.91 %
Rwork0.157 150743 -
obs0.159 158530 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.59 Å2 / Biso mean: 39.37 Å2 / Biso min: 17.71 Å2
Refinement stepCycle: final / Resolution: 2.22→86.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19461 0 189 1768 21418
Biso mean--59.78 46.2 -
Num. residues----2416
Refine LS restraints NCS
Ens-IDDom-IDNumberRefine-IDTypeRms dev position (Å)
210X-RAY DIFFRACTIONPOSITIONAL0
220X-RAY DIFFRACTIONPOSITIONAL0
310X-RAY DIFFRACTIONPOSITIONAL0
320X-RAY DIFFRACTIONPOSITIONAL0
410X-RAY DIFFRACTIONPOSITIONAL0
420X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.240.29682350.25844543477890
2.24-2.270.2982760.250849765252100
2.27-2.30.26532690.23465007527699
2.3-2.320.28182530.229750325285100
2.32-2.360.27162440.225949925236100
2.36-2.390.28392870.22125002528999
2.39-2.420.2892320.218550155247100
2.42-2.460.25482760.20535000527699
2.46-2.50.27012470.20455069531699
2.5-2.540.24142270.194650545281100
2.54-2.580.24452580.18450025260100
2.58-2.630.2482530.18650455298100
2.63-2.680.24592430.179850485291100
2.68-2.730.23162830.170950005283100
2.73-2.790.2282540.170450815335100
2.79-2.860.24822550.172750415296100
2.86-2.930.262450.18445072531799
2.93-3.010.22732700.17515009527999
3.01-3.10.21542460.16785031527799
3.1-3.20.21372860.16134918520496
3.2-3.310.18092790.15374930520999
3.31-3.440.19682980.149950375335100
3.44-3.60.17782840.1550635347100
3.6-3.790.19442420.135151285370100
3.79-4.030.15352560.118450785334100
4.03-4.340.14912610.11515115537699
4.34-4.780.14152640.11355106537099
4.78-5.470.15572660.12525099536598
5.47-6.890.19272630.14595039530296
6.89-86.10.20232350.15465211544695

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