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- PDB-6ydu: XFEL structure of the Soluble methane monooxygenase hydroxylase a... -

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Basic information

Entry
Database: PDB / ID: 6ydu
TitleXFEL structure of the Soluble methane monooxygenase hydroxylase and regulatory subunit complex, from Methylosinus trichosporium OB3b, reoxidized diferric state, 10s O2 exposure.
Components
  • (Methane monooxygenase ...) x 2
  • (Methane monooxygenase) x 2
KeywordsOXIDOREDUCTASE / Ferritin superfamily / Soluble methane monooxygenase / Di-iron oxygen activation / Substrate oxidation.
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
: / Methane monooxygenase / Methane monooxygenase / Methane monooxygenase / Methane monooxygenase component A alpha chain / Methane monooxygenase regulatory protein B
Similarity search - Component
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSrinivas, V. / Hogbom, M.
Funding support Sweden, United States, United Kingdom, 15items
OrganizationGrant numberCountry
Swedish Research Council2017-04018 Sweden
European Research Council (ERC)HIGH-GEAR 724394 Sweden
Knut and Alice Wallenberg Foundation2012.0233 Sweden
Knut and Alice Wallenberg Foundation2017.0275 Sweden
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)GM08347 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133081 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117126 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM126289 United States
Biotechnology and Biological Sciences Research Council (BBSRC)102593 United Kingdom
Wellcome Trust210734/Z/18/Z United Kingdom
Royal SocietyRSWF-R2-182017 United Kingdom
Department of Energy (DOE, United States)DOE BES DE-AC02-05CH11231 United States
Department of Energy (DOE, United States)DOE BES DE-AC02-76SF00515 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2020
Title: High-Resolution XFEL Structure of the Soluble Methane Monooxygenase Hydroxylase Complex with its Regulatory Component at Ambient Temperature in Two Oxidation States.
Authors: Srinivas, V. / Banerjee, R. / Lebrette, H. / Jones, J.C. / Aurelius, O. / Kim, I.S. / Pham, C.C. / Gul, S. / Sutherlin, K.D. / Bhowmick, A. / John, J. / Bozkurt, E. / Fransson, T. / Aller, P. ...Authors: Srinivas, V. / Banerjee, R. / Lebrette, H. / Jones, J.C. / Aurelius, O. / Kim, I.S. / Pham, C.C. / Gul, S. / Sutherlin, K.D. / Bhowmick, A. / John, J. / Bozkurt, E. / Fransson, T. / Aller, P. / Butryn, A. / Bogacz, I. / Simon, P. / Keable, S. / Britz, A. / Tono, K. / Kim, K.S. / Park, S.Y. / Lee, S.J. / Park, J. / Alonso-Mori, R. / Fuller, F.D. / Batyuk, A. / Brewster, A.S. / Bergmann, U. / Sauter, N.K. / Orville, A.M. / Yachandra, V.K. / Yano, J. / Lipscomb, J.D. / Kern, J. / Hogbom, M.
History
DepositionMar 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
B: Methane monooxygenase
D: Methane monooxygenase component A alpha chain
F: Methane monooxygenase
G: Methane monooxygenase regulatory protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,8727
Polymers139,6684
Non-polymers2043
Water8,431468
1
B: Methane monooxygenase
D: Methane monooxygenase component A alpha chain
F: Methane monooxygenase
G: Methane monooxygenase regulatory protein B
hetero molecules

B: Methane monooxygenase
D: Methane monooxygenase component A alpha chain
F: Methane monooxygenase
G: Methane monooxygenase regulatory protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,74314
Polymers279,3368
Non-polymers4086
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area56320 Å2
ΔGint-274 kcal/mol
Surface area65880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.922, 106.922, 304.082
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-620-

HOH

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Components

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Protein , 2 types, 2 molecules BF

#1: Protein Methane monooxygenase


Mass: 45295.340 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A1A6FHH2, UniProt: A0A2D2D0T0*PLUS

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Methane monooxygenase ... , 2 types, 2 molecules DG

#2: Protein Methane monooxygenase component A alpha chain / Methane hydroxylase


Mass: 60031.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: P27353, methane monooxygenase (soluble)
#4: Protein Methane monooxygenase regulatory protein B


Mass: 14896.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: mmoB / Production host: Escherichia coli (E. coli) / References: UniProt: P27356

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Non-polymers , 3 types, 471 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30 mM Sodium-Iodide, 30 mM Sodium-Bromide, 30 mM Sodium-Fluoride, 20% (v/v) Glycerol, 10% (w/v) PEG 4000, 100 mM HEPES/MOPS pH 7.5 10 mM Iron(III) chloride
Temp details: Room temprature

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.30396 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.30396 Å / Relative weight: 1
ReflectionResolution: 1.95→33.96 Å / Num. obs: 128969 / % possible obs: 99.98 % / Redundancy: 74.36 % / Biso Wilson estimate: 41.91 Å2 / CC1/2: 0.945 / Net I/σ(I): 25.196
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 12712 / CC1/2: 0.077 / % possible all: 99.16
Serial crystallography measurementCollection time total: 0.66 hours / Collimation: compound refractive lenses / Focal spot size: 4 µm2 / Pulse duration: 35 fsec. / Pulse energy: 4000 µJ / Pulse photon energy: 9.508 keV / XFEL pulse repetition rate: 20 Hz
Serial crystallography sample deliveryDescription: drop on tape combined with acustic droplet ejection
Method: injection
Serial crystallography sample delivery injectionCarrier solvent: mother liquour / Description: acustic droplet ejection / Flow rate: 8 µL/min / Injector temperature: 298.15 K / Jet diameter: 230 µm / Power by: focused acoustic pulse
Serial crystallography data reductionFrames total: 48000 / Lattices indexed: 15629 / XFEL run numbers: 283-290

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
cctbx.xfeldata reduction
PHASERphasing
cxi.mergedata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YD0

6yd0


Resolution: 1.95→33.71 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1968 2000 1.55 %
Rwork0.1687 126813 -
obs0.1691 128969 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.41 Å2 / Biso mean: 46.4498 Å2 / Biso min: 27.76 Å2
Refinement stepCycle: final / Resolution: 1.95→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9725 0 8 468 10201
Biso mean--49.93 49.41 -
Num. residues----1207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.38881400.35768824896499
2-2.050.36021410.318689529093100
2.05-2.110.29471410.288989109051100
2.11-2.180.27761420.268989749116100
2.18-2.260.31321410.241689389079100
2.26-2.350.26181410.221389719112100
2.35-2.460.24941410.20389909131100
2.46-2.590.22671420.194789999141100
2.59-2.750.23081430.178390709213100
2.75-2.960.2021430.16390469189100
2.96-3.260.20171430.160590809223100
3.26-3.730.16361440.141491549298100
3.73-4.70.13961450.126392629407100
4.7-33.960.17791530.154196439796100

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