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- PDB-6vk6: Crystal Structure of Methylosinus trichosporium OB3b Soluble Meth... -

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Basic information

Entry
Database: PDB / ID: 6vk6
TitleCrystal Structure of Methylosinus trichosporium OB3b Soluble Methane Monooxygenase Hydroxylase
Components
  • (Methane monooxygenase) x 2
  • Methane monooxygenase component A alpha chain
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
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 ...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 component A alpha chain / Methane monooxygenase / Methane monooxygenase component A alpha chain
Similarity search - Component
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.52 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
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
C: Methane monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,63151
Polymers124,7713
Non-polymers2,86048
Water20,2491124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25540 Å2
ΔGint-21 kcal/mol
Surface area34690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.071, 292.634, 141.786
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-613-

HOH

21B-814-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Methane monooxygenase component A alpha chain


Mass: 60031.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methylosinus trichosporium OB3b (bacteria)
References: UniProt: A0A2D2D5X0, UniProt: P27353*PLUS
#2: 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: A0A2D2D0T0

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Non-polymers , 4 types, 1172 molecules

#4: 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
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1124 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tacsimate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.52→141.79 Å / Num. obs: 395118 / % possible obs: 98.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.6
Reflection shellResolution: 1.52→1.55 Å / Num. unique obs: 9633 / CC1/2: 0.509 / Rpim(I) all: 0.692

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
PHENIXphasing
PHENIXdata scaling
PHENIXdata processing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1MHZ

1mhz


Resolution: 1.52→65.01 Å / SU ML: 0.2029 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.9505
RfactorNum. reflection% reflection
Rfree0.1636 18031 4.94 %
Rwork0.1464 --
obs0.1473 364838 93.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.77 Å2
Refinement stepCycle: LAST / Resolution: 1.52→65.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8686 0 174 1124 9984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00489206
X-RAY DIFFRACTIONf_angle_d0.85212440
X-RAY DIFFRACTIONf_chiral_restr0.06561277
X-RAY DIFFRACTIONf_plane_restr0.00531605
X-RAY DIFFRACTIONf_dihedral_angle_d16.10773314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.3645750.361811032X-RAY DIFFRACTION88.56
1.54-1.560.34446180.331711770X-RAY DIFFRACTION95.73
1.56-1.570.33546090.331412054X-RAY DIFFRACTION97.12
1.57-1.590.31736580.311711929X-RAY DIFFRACTION96.61
1.59-1.620.31796050.295711921X-RAY DIFFRACTION96.24
1.62-1.640.31365630.28511759X-RAY DIFFRACTION95.63
1.64-1.660.29876420.281311881X-RAY DIFFRACTION95.51
1.66-1.690.27596060.269111600X-RAY DIFFRACTION94.28
1.69-1.710.2736140.257411601X-RAY DIFFRACTION94.05
1.71-1.740.25845930.24711597X-RAY DIFFRACTION93.3
1.74-1.770.25335860.241811285X-RAY DIFFRACTION91.88
1.77-1.80.25845960.237410851X-RAY DIFFRACTION87.12
1.8-1.840.2525930.230310775X-RAY DIFFRACTION88.14
1.84-1.870.22815920.206411957X-RAY DIFFRACTION96.26
1.87-1.920.19585640.182312028X-RAY DIFFRACTION96.24
1.92-1.960.18896640.168211747X-RAY DIFFRACTION95.82
1.96-2.010.17227090.152111762X-RAY DIFFRACTION96.24
2.01-2.060.17456310.140611864X-RAY DIFFRACTION95.86
2.06-2.120.16376120.134111813X-RAY DIFFRACTION95.44
2.12-2.190.14876010.123211605X-RAY DIFFRACTION94.02
2.19-2.270.13455550.11411148X-RAY DIFFRACTION89.99
2.27-2.360.12586010.108410794X-RAY DIFFRACTION87.48
2.36-2.470.13215890.106211967X-RAY DIFFRACTION96.55
2.47-2.60.1356080.104311907X-RAY DIFFRACTION96.25
2.6-2.760.12615710.106111868X-RAY DIFFRACTION95.63
2.76-2.980.12985540.109911641X-RAY DIFFRACTION93.86
2.98-3.270.13254950.119211002X-RAY DIFFRACTION88.35
3.27-3.750.1285900.117711055X-RAY DIFFRACTION89.37
3.75-4.720.10176550.101811576X-RAY DIFFRACTION94.11
4.72-65.010.15175820.138311018X-RAY DIFFRACTION88.97
Refinement TLS params.Method: refined / Origin x: 23.432323238 Å / Origin y: 36.0316160163 Å / Origin z: 8.33869830243 Å
111213212223313233
T0.139289564204 Å24.80737947498E-5 Å20.00214997832326 Å2-0.238126755421 Å2-0.00218642821743 Å2--0.165772938965 Å2
L0.0578997331169 °2-0.0266315388449 °20.0128102787762 °2-0.219183200827 °2-0.0298082661988 °2--0.0981614746929 °2
S0.0025013833957 Å °0.0164332580508 Å °0.00465058470005 Å °-0.02358095225 Å °-0.00557047546414 Å °-0.0021545583626 Å °0.0127954791177 Å °0.00969204335264 Å °0.00588713187121 Å °
Refinement TLS groupSelection details: all

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