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- PDB-7tcu: Methanobactin biosynthetic protein complex of MbnB and MbnC from ... -

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Basic information

Entry
Database: PDB / ID: 7tcu
TitleMethanobactin biosynthetic protein complex of MbnB and MbnC from Methylosinus trichosporium OB3b at 2.31 Angstrom resolution
Components
  • Methanobactin biosynthesis cassette protein MbnB
  • Methanobactin biosynthesis cassette protein MbnC
KeywordsBIOSYNTHETIC PROTEIN / Metalloprotein / Natural product biosynthetic protein / Complex
Function / homology
Function and homology information


Conserved hypothetical protein CHP04061, AZL007950 / Methanobactin biosynthesis cassette protein MbnB / Uncharacterised protein family UPF0276 / RiPP precursor modification enzyme MbnB/TglH/ChrH / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Methanobactin biosynthesis cassette protein MbnC / Methanobactin biosynthesis cassette protein MbnB
Similarity search - Component
Biological speciesMethylosinus trichosporium OB3b (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsPark, Y. / Reyes, R.M. / Rosenzweig, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118035 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: A mixed-valent Fe(II)Fe(III) species converts cysteine to an oxazolone/thioamide pair in methanobactin biosynthesis.
Authors: Park, Y.J. / Jodts, R.J. / Slater, J.W. / Reyes, R.M. / Winton, V.J. / Montaser, R.A. / Thomas, P.M. / Dowdle, W.B. / Ruiz, A. / Kelleher, N.L. / Bollinger Jr., J.M. / Krebs, C. / Hoffman, B. ...Authors: Park, Y.J. / Jodts, R.J. / Slater, J.W. / Reyes, R.M. / Winton, V.J. / Montaser, R.A. / Thomas, P.M. / Dowdle, W.B. / Ruiz, A. / Kelleher, N.L. / Bollinger Jr., J.M. / Krebs, C. / Hoffman, B.M. / Rosenzweig, A.C.
History
DepositionDec 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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: Methanobactin biosynthesis cassette protein MbnB
B: Methanobactin biosynthesis cassette protein MbnB
C: Methanobactin biosynthesis cassette protein MbnC
D: Methanobactin biosynthesis cassette protein MbnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,64712
Polymers107,1204
Non-polymers5278
Water3,819212
1
A: Methanobactin biosynthesis cassette protein MbnB
D: Methanobactin biosynthesis cassette protein MbnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8236
Polymers53,5602
Non-polymers2644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-77 kcal/mol
Surface area19110 Å2
MethodPISA
2
B: Methanobactin biosynthesis cassette protein MbnB
C: Methanobactin biosynthesis cassette protein MbnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8236
Polymers53,5602
Non-polymers2644
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-82 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.670, 215.680, 215.624
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
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

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Components

#1: Protein Methanobactin biosynthesis cassette protein MbnB


Mass: 31322.469 Da / Num. of mol.: 2 / Mutation: E67A, E69A, K70A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: mbnB, CQW49_07160 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D2D5M1
#2: Protein Methanobactin biosynthesis cassette protein MbnC


Mass: 22237.408 Da / Num. of mol.: 2 / Mutation: E162A, E164A, K165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylosinus trichosporium OB3b (bacteria)
Gene: mbnC, CQW49_07155 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2D2CY73
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris propane, pH 7.0, 20-26% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.722 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.722 Å / Relative weight: 1
ReflectionResolution: 2.31→49.33 Å / Num. obs: 52288 / % possible obs: 99.1 % / Redundancy: 3.458 % / Biso Wilson estimate: 45.98 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.108 / Χ2: 0.964 / Net I/σ(I): 8.49 / Num. measured all: 341251
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.31-2.373.4350.6911.723926728369650.8020.81795.6
2.37-2.443.4210.5522.224549720571750.8640.65499.6
2.44-2.513.4030.4242.8423820701669990.8960.50499.8
2.51-2.593.3660.3643.4322637674667260.9030.43599.7
2.59-2.673.2250.2714.1521239663465850.9370.32699.3
2.67-2.772.9610.2054.9618269635761700.9550.25297.1
2.77-2.873.5660.1646.8421903615061420.9710.19499.9
2.87-2.993.5770.1387.9221185593559220.9780.16299.8
2.99-3.123.5750.1139.620066562556130.9810.13299.8
3.12-3.273.5950.09910.919350539853820.9840.11699.7
3.27-3.453.5940.08812.2518439517451310.9860.10399.2
3.45-3.663.5880.08113.4117457488848660.9870.09599.5
3.66-3.913.5680.07614.2316273458545610.9890.08999.5
3.91-4.223.4520.07414.6514590424942260.9880.08799.5
4.22-4.633.2530.06914.6712635392538840.9880.08299
4.63-5.173.1260.06714.4710707351634250.9870.08297.4
5.17-5.973.8620.07115.9312019311231120.9910.083100
5.97-7.323.8620.0716.1510323267326730.9910.081100
7.32-10.353.8510.06617.37840203620360.9920.077100
10.35-49.333.6820.06417.174024111410930.990.07698.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7TCR

7tcr


Resolution: 2.31→49.33 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1998 3.85 %
Rwork0.202 49925 -
obs0.2038 51923 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.74 Å2 / Biso mean: 47.4336 Å2 / Biso min: 27.2 Å2
Refinement stepCycle: final / Resolution: 2.31→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7442 0 16 212 7670
Biso mean--62.16 45.54 -
Num. residues----915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.370.37651330.37773333346695
2.37-2.440.36551430.31735413684100
2.44-2.510.31291400.269535303670100
2.51-2.590.30031410.269535333674100
2.59-2.680.34371410.26713542368399
2.68-2.790.31481400.27693509364999
2.79-2.910.31921440.289935723716100
2.91-3.070.27261420.251835583700100
3.07-3.260.2951430.225535653708100
3.26-3.510.27271430.209835853728100
3.51-3.870.24471440.178835973741100
3.87-4.420.19741460.146136223768100
4.42-5.570.18371450.14563625377099
5.57-49.330.19771530.163138133966100
Refinement TLS params.Method: refined / Origin x: 11.0364 Å / Origin y: 2.5851 Å / Origin z: 81.1683 Å
111213212223313233
T0.2805 Å2-0.0523 Å20.0045 Å2-0.2658 Å2-0.0073 Å2--0.3372 Å2
L0.288 °2-0.5172 °2-0.0009 °2-1.674 °20.1873 °2--0.2959 °2
S-0.0091 Å °0.0201 Å °0.0324 Å °0.0698 Å °-0.0271 Å °0.0646 Å °-0.0347 Å °0.0154 Å °0.0339 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 263
2X-RAY DIFFRACTION1allB1 - 263
3X-RAY DIFFRACTION1allC1 - 195
4X-RAY DIFFRACTION1allD2 - 195
5X-RAY DIFFRACTION1allE1 - 6
6X-RAY DIFFRACTION1allS1 - 249
7X-RAY DIFFRACTION1allF1 - 2

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