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- PDB-7s6q: Complex structure of Methane monooxygenase hydroxylase and regula... -

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Basic information

Entry
Database: PDB / ID: 7s6q
TitleComplex structure of Methane monooxygenase hydroxylase and regulatory subunit DBL2
Components(Methane monooxygenase ...) x 4
KeywordsOXIDOREDUCTASE / RESOLVASE
Function / homology
Function and homology information


methane metabolic process / 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 / monooxygenase activity / metal ion binding
Similarity search - Function
: / Monooxygenase component MmoB/DmpM / Phenol Hydroxylase P2 Protein / 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 / Phenol Hydroxylase P2 Protein / 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 / Alpha-Beta Complex / Alpha Beta
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: 1.96 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)276,91042
Polymers274,7048
Non-polymers2,20634
Water32,6431812
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60950 Å2
ΔGint-176 kcal/mol
Surface area64610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.176, 105.358, 297.809
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 320 or resid 322 through 395))
21(chain F and (resid 4 through 320 or resid 322 through 395))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEU(chain B and (resid 4 through 320 or resid 322 through 395))BB4 - 3201 - 317
12ALAALAASNASN(chain B and (resid 4 through 320 or resid 322 through 395))BB322 - 395319 - 392
21PROPROLEULEU(chain F and (resid 4 through 320 or resid 322 through 395))FF4 - 3201 - 317
22ALAALAASNASN(chain F and (resid 4 through 320 or resid 322 through 395))FF322 - 395319 - 392

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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, Oxidoreductases
#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: 14118.995 Da / Num. of mol.: 2 / Mutation: S109A, T111A
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, 1846 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-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#7: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1812 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 20% PEG3350, 0.2 M sodium phosphate dibasic, pH 8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.96→148.9 Å / Num. obs: 225895 / % possible obs: 98.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 32.93 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.076 / Rrim(I) all: 0.142 / Net I/σ(I): 6.7 / Num. measured all: 705096
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
1.96-1.993.21.835457112360.2921.1792.1640.699.7
10.74-148.93.10.045470615140.9970.0290.05424.496

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 7M8R

7m8r


Resolution: 1.96→148.9 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2267 10683 4.87 %
Rwork0.1859 208623 -
obs0.1879 219306 95.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.34 Å2 / Biso mean: 35.8289 Å2 / Biso min: 17.35 Å2
Refinement stepCycle: final / Resolution: 1.96→148.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19413 0 134 1820 21367
Biso mean--48.73 41.17 -
Num. residues----2407
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B3761X-RAY DIFFRACTION6.058TORSIONAL
12F3761X-RAY DIFFRACTION6.058TORSIONAL
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 (%)
1.96-1.980.36622680.33394593486164
1.98-2.010.38462260.334972519869
2.01-2.030.33713160.32866415673189
2.03-2.060.36613680.3186873724195
2.06-2.080.32053870.30746989737698
2.08-2.110.34373640.3057124748898
2.11-2.140.37313890.28996915730496
2.14-2.170.30863800.27826982736296
2.17-2.210.32043550.26187194754999
2.21-2.240.30253900.25297167755799
2.24-2.280.30333890.25047185757499
2.28-2.320.29023560.24457248760499
2.32-2.370.30743390.2277199753899
2.37-2.420.26623480.22297161750999
2.42-2.470.27313350.22337216755199
2.47-2.530.27543760.22257176755299
2.53-2.590.29613240.21297041736597
2.59-2.660.26643470.19486893724094
2.66-2.740.25323520.18747240759299
2.74-2.830.23783740.18287278765299
2.83-2.930.24134040.18737186759099
2.93-3.050.23083460.18747223756999
3.05-3.180.22533510.18177274762599
3.18-3.350.21293440.17337115745997
3.35-3.560.21213780.17096893727194
3.56-3.840.19423530.15587302765599
3.84-4.220.16073880.13067241762998
4.22-4.830.13763540.12217190754497
4.83-6.090.17513770.14027039741694
6.09-148.90.18554050.1637299770494

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