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- PDB-7s6s: Complex structure of Methane monooxygenase hydroxylase and regula... -

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Basic information

Entry
Database: PDB / ID: 7s6s
TitleComplex structure of Methane monooxygenase hydroxylase and regulatory subunit DBL1
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: 1.98 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)279,24864
Polymers275,6778
Non-polymers3,57156
Water36,9492051
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area65750 Å2
ΔGint-113 kcal/mol
Surface area66040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.730, 105.710, 299.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 14605.560 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 , 4 types, 2107 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.: 2051 / 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: 58.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1% 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: 1.98→73.67 Å / Num. obs: 222638 / % possible obs: 98.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 30.47 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.071 / Rrim(I) all: 0.168 / Net I/σ(I): 7.6 / Num. measured all: 1139865 / Scaling rejects: 1734
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.98-2.0151.42455172109500.5440.6641.5771.698.8
10.84-73.675.10.037746414510.9980.0170.04120.395.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 7M8Q

7m8q


Resolution: 1.98→73.67 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1885 11103 4.99 %
Rwork0.1542 211422 -
obs0.1559 222525 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.22 Å2 / Biso mean: 31.0344 Å2 / Biso min: 15.15 Å2
Refinement stepCycle: final / Resolution: 1.98→73.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19456 0 222 2057 21735
Biso mean--49.92 41.14 -
Num. residues----2417
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 (%)
1.98-20.31533790.27966977735699
2-2.030.33143250.26347059738499
2.03-2.050.27313390.24846880721997
2.05-2.080.28223770.24936837721496
2.08-2.10.2933490.23797003735299
2.1-2.130.26753540.22167054740899
2.13-2.160.24993730.21417028740199
2.16-2.20.25183340.19767086742099
2.2-2.230.23623710.18947000737199
2.23-2.270.2713550.22147042739798
2.27-2.310.21713680.17737048741699
2.31-2.350.23383840.16847035741999
2.35-2.390.21093870.16077000738799
2.39-2.440.193910.15827005739699
2.44-2.490.20423840.15817051743599
2.49-2.550.19773900.15737052744299
2.55-2.620.20563570.1557083744099
2.62-2.690.18783990.15267054745399
2.69-2.770.1913900.1517039742999
2.77-2.860.1913750.14427076745199
2.86-2.960.18484090.14836799720896
2.96-3.080.20223990.15017014741398
3.08-3.220.1943830.15227064744798
3.22-3.390.19183090.15237094740398
3.39-3.60.17393730.14077073744698
3.6-3.880.16413170.13167140745798
3.88-4.270.14793830.11957108749198
4.27-4.880.12273590.11397213757299
4.88-6.150.16463970.13217109750697
6.15-73.670.16123930.1497399779297

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