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- PDB-7s6t: Complex structure of Methane monooxygenase hydroxylase and regula... -

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Basic information

Entry
Database: PDB / ID: 7s6t
TitleComplex structure of Methane monooxygenase hydroxylase and regulatory subunit H33A
Components(Methane monooxygenase ...) x 4
KeywordsHYDROLASE / OXIDOREDUCTASE
Function / homology
Function and homology information


methane monooxygenase [NAD(P)H] 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 / 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 / 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 / : / 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: 1.82 Å
AuthorsJohns, J.C. / Banerjee, R. / Semonis, M.M. / Shi, K. / Aihara, H. / 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: 2022
Title: X-ray Crystal Structures of Methane Monooxygenase Hydroxylase Complexes with Variants of Its Regulatory Component: Correlations with Altered Reaction Cycle Dynamics.
Authors: Jones, J.C. / Banerjee, R. / Semonis, M.M. / Shi, K. / Aihara, H. / Lipscomb, J.D.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)279,26064
Polymers275,6898
Non-polymers3,57156
Water40,2642235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area66050 Å2
ΔGint-104 kcal/mol
Surface area66000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.520, 105.600, 299.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 4 through 139 or resid 141...
21(chain F and (resid 4 through 139 or resid 141...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain B and (resid 4 through 139 or resid 141...B4 - 139
121(chain B and (resid 4 through 139 or resid 141...B141 - 320
131(chain B and (resid 4 through 139 or resid 141...B322
141(chain B and (resid 4 through 139 or resid 141...B4 - 1201
151(chain B and (resid 4 through 139 or resid 141...B4 - 1201
161(chain B and (resid 4 through 139 or resid 141...B4 - 1201
171(chain B and (resid 4 through 139 or resid 141...B4 - 1201
181(chain B and (resid 4 through 139 or resid 141...B4 - 1201
191(chain B and (resid 4 through 139 or resid 141...B4 - 1201
211(chain F and (resid 4 through 139 or resid 141...F4 - 139
221(chain F and (resid 4 through 139 or resid 141...F141 - 320
231(chain F and (resid 4 through 139 or resid 141...F322 - 394
241(chain F and (resid 4 through 139 or resid 141...F395
251(chain F and (resid 4 through 139 or resid 141...F4 - 604
261(chain F and (resid 4 through 139 or resid 141...F4 - 604
271(chain F and (resid 4 through 139 or resid 141...F4 - 604
281(chain F and (resid 4 through 139 or resid 141...F4 - 604

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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: 14611.542 Da / Num. of mol.: 2 / Mutation: H33A
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 , 4 types, 2291 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 50 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2235 / 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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 21% PEG3350 and 0.2 M Na2HPO4 pH 6.6

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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 EIGER X 16M / 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: 1.82→48.51 Å / Num. obs: 289411 / % possible obs: 99.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 28.84 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.046 / Rrim(I) all: 0.105 / Net I/σ(I): 9.3 / Num. measured all: 1472673 / Scaling rejects: 111
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.079 / Num. unique obs: 13878 / CC1/2: 0.736 / Rpim(I) all: 0.519 / Rrim(I) all: 1.2 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 7M8Q

7m8q


Resolution: 1.82→48.51 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1722 14175 4.9 %
Rwork0.1462 275111 -
obs0.1475 289286 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 190.18 Å2 / Biso mean: 31.4446 Å2 / Biso min: 16.34 Å2
Refinement stepCycle: final / Resolution: 1.82→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19456 0 222 2241 21919
Biso mean--51.07 42.67 -
Num. residues----2417
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B3740X-RAY DIFFRACTION4.479TORSIONAL
12F3740X-RAY DIFFRACTION4.479TORSIONAL
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 (%)
1.82-1.840.29034280.24988759918796
1.84-1.860.26474680.234691509618100
1.86-1.880.26064750.222791549629100
1.88-1.910.25154820.216290889570100
1.91-1.930.24814960.202291329628100
1.93-1.960.22885020.200190799581100
1.96-1.990.22874700.184691439613100
1.99-2.020.21644320.177691909622100
2.02-2.050.2124530.169991649617100
2.05-2.080.2184430.167791359578100
2.08-2.120.20214570.159591699626100
2.12-2.160.18954710.156891489619100
2.16-2.20.19295070.154491549661100
2.2-2.240.18664750.151590939568100
2.24-2.290.20344690.155191569625100
2.29-2.350.20284890.155191359624100
2.35-2.40.1894750.148991739648100
2.4-2.470.1854650.14791199584100
2.47-2.540.19414840.15269161964599
2.54-2.620.18155330.14819105963899
2.62-2.720.1634690.13759174964399
2.72-2.830.16585040.1399131963599
2.83-2.950.17984970.14429147964499
2.95-3.110.19195000.15179185968599
3.11-3.310.174400.14679265970599
3.31-3.560.16464460.14329244969099
3.56-3.920.14754360.12979292972899
3.92-4.480.13014910.11629243973499
4.48-5.650.13754640.12249377984199
5.65-48.510.14024540.144396461010098

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