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- PDB-6cxh: Crystal structure of particulate methane monooxygenase from Methy... -

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Basic information

Entry
Database: PDB / ID: 6cxh
TitleCrystal structure of particulate methane monooxygenase from Methylomicrobium alcaliphilum 20Z
Components
  • Particulate methane monooxygenase, A subunitMethane monooxygenase (particulate)
  • Particulate methane monooxygenase, B subunitMethane monooxygenase (particulate)
  • Particulate methane monooxygenase, C subunitMethane monooxygenase (particulate)
KeywordsOXIDOREDUCTASE / copper dependent methane monooxygenase
Function / homology
Function and homology information


methane monooxygenase (soluble) / methane monooxygenase NADH activity / methane monooxygenase NADPH activity / membrane
Similarity search - Function
Helix hairpin bin / particulate methane monooxygenase, chain B / Ammonia/particulate methane monooxygenase, subunit A / Particulate methane monooxygenase, b subunit. Chain: A, domain 3 / Particulate methane monooxygenase, b subunit. Chain: A, domain 1 / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily ...Helix hairpin bin / particulate methane monooxygenase, chain B / Ammonia/particulate methane monooxygenase, subunit A / Particulate methane monooxygenase, b subunit. Chain: A, domain 3 / Particulate methane monooxygenase, b subunit. Chain: A, domain 1 / Ammonia monooxygenase/particulate methane monooxygenase, subunit A / Ammonia monooxygenase/particulate methane monooxygenase, subunit C / Ammonia/methane monooxygenase, subunit B, hairpin domain superfamily / Ammonia/methane monooxygenase, subunit B, C-terminal / Ammonia monooxygenase/particulate methane monooxygenase, subunit C domain superfamily / Ammonia/particulate methane monooxygenase, subunit A superfamily / Ammonia monooxygenase / Ammonia monooxygenase/methane monooxygenase, subunit C / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein / Helix Hairpins / Jelly Rolls / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / Particulate methane monooxygenase, C subunit / Particulate methane monooxygenase, A subunit / Particulate methane monooxygenase, B subunit
Similarity search - Component
Biological speciesMethylomicrobium alcaliphilum 20Z (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsRo, S.Y. / Rosenzweig, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM118035 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5T32GM008382 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: From micelles to bicelles: Effect of the membrane on particulate methane monooxygenase activity.
Authors: Ro, S.Y. / Ross, M.O. / Deng, Y.W. / Batelu, S. / Lawton, T.J. / Hurley, J.D. / Stemmler, T.L. / Hoffman, B.M. / Rosenzweig, A.C.
History
DepositionApr 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

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Assembly

Deposited unit
A: Particulate methane monooxygenase, B subunit
B: Particulate methane monooxygenase, A subunit
C: Particulate methane monooxygenase, C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8076
Polymers102,7543
Non-polymers1,0533
Water0
1
A: Particulate methane monooxygenase, B subunit
B: Particulate methane monooxygenase, A subunit
C: Particulate methane monooxygenase, C subunit
hetero molecules

A: Particulate methane monooxygenase, B subunit
B: Particulate methane monooxygenase, A subunit
C: Particulate methane monooxygenase, C subunit
hetero molecules

A: Particulate methane monooxygenase, B subunit
B: Particulate methane monooxygenase, A subunit
C: Particulate methane monooxygenase, C subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,42118
Polymers308,2639
Non-polymers3,1589
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_245-y-3,x-y-1,z1
crystal symmetry operation3_325-x+y-2,-x-3,z1
Buried area51620 Å2
ΔGint-427 kcal/mol
Surface area78870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.840, 143.840, 146.152
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Particulate methane monooxygenase, B subunit / Methane monooxygenase (particulate)


Mass: 45602.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methylomicrobium alcaliphilum 20Z (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
References: UniProt: G4SZ64, methane monooxygenase (soluble)
#2: Protein Particulate methane monooxygenase, A subunit / Methane monooxygenase (particulate)


Mass: 28277.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methylomicrobium alcaliphilum 20Z (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
References: UniProt: G4SZ63, methane monooxygenase (soluble)
#3: Protein Particulate methane monooxygenase, C subunit / Methane monooxygenase (particulate)


Mass: 28874.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Methylomicrobium alcaliphilum 20Z (bacteria)
Strain: DSM 19304 / NCIMB 14124 / VKM B-2133 / 20Z
References: UniProt: G4SZ62, methane monooxygenase (soluble)
#4: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM

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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: 4.25 Å3/Da / Density % sol: 71.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.8 M AmSO4, 0.2 M MES, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033288, 1.377602
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0332881
21.3776021
ReflectionResolution: 2.7→40 Å / Num. obs: 46989 / % possible obs: 99.1 % / Redundancy: 9 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.07 / Net I/σ(I): 40.6
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 11.2 / CC1/2: 0.984 / Rpim(I) all: 0.22 / Rrim(I) all: 0.588 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-20002.3.10data reduction
HKL-20002.3.10data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RGB

3rgb


Resolution: 2.704→39.579 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.27
RfactorNum. reflection% reflection
Rfree0.2678 2339 5.06 %
Rwork0.2133 --
obs0.2161 35187 99.151 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.704→39.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5738 0 69 0 5807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015984
X-RAY DIFFRACTIONf_angle_d1.3138156
X-RAY DIFFRACTIONf_dihedral_angle_d11.4373387
X-RAY DIFFRACTIONf_chiral_restr0.065908
X-RAY DIFFRACTIONf_plane_restr0.0081002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.704-2.77710.42330.2833158X-RAY DIFFRACTION4
2.7771-2.85880.2908160.3032481X-RAY DIFFRACTION14
2.8588-2.9510.3048360.2606908X-RAY DIFFRACTION26
2.951-3.05640.3692770.25411592X-RAY DIFFRACTION46
3.0564-3.17880.3831520.26522868X-RAY DIFFRACTION85
3.1788-3.32340.29871730.24853441X-RAY DIFFRACTION100
3.3234-3.49850.26722030.23183391X-RAY DIFFRACTION100
3.4985-3.71750.2581880.21253405X-RAY DIFFRACTION100
3.7175-4.00430.24991680.19373431X-RAY DIFFRACTION100
4.0043-4.40680.261950.18143405X-RAY DIFFRACTION100
4.4068-5.04330.22561850.17583443X-RAY DIFFRACTION100
5.0433-6.34980.25791880.21543433X-RAY DIFFRACTION100
6.3498-39.58320.26151970.2253450X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -168.5951 Å / Origin y: -171.7598 Å / Origin z: 8.9381 Å
111213212223313233
T0.0701 Å2-0.2034 Å2-0.0151 Å2-0.0705 Å20.0439 Å2--0.0385 Å2
L0.029 °20.0458 °20.0067 °2-0.0392 °20.0044 °2--0.009 °2
S0.0408 Å °0.0329 Å °0.0044 Å °0.0166 Å °-0.0643 Å °0.0298 Å °-0.004 Å °-0.0521 Å °-0.0195 Å °
Refinement TLS groupSelection details: all

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