[English] 日本語
Yorodumi
- PDB-7tcx: Methanobactin biosynthetic protein complex of MbnB and MbnC from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tcx
TitleMethanobactin biosynthetic protein complex of MbnB and MbnC from Methylosinus trichosporium OB3b at 2.21 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: 2.21 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water6,179343
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 area4890 Å2
ΔGint-82 kcal/mol
Surface area19130 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 area4960 Å2
ΔGint-84 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.655, 216.025, 216.148
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

-
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: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 293 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

-
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: 2.21→48.33 Å / Num. obs: 60054 / % possible obs: 98.9 % / Redundancy: 6.921 % / Biso Wilson estimate: 38.93 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rrim(I) all: 0.122 / Χ2: 1.008 / Net I/σ(I): 12.31 / Num. measured all: 784357
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
2.21-2.276.9051.0552.8154118848378380.9111.1492.4
2.27-2.337.0620.8793.5657109824380870.9290.94898.1
2.33-2.46.9770.674.5155973805580230.9480.72399.6
2.4-2.476.9820.5335.4653646776376840.9680.57599
2.47-2.556.850.4156.651522759475220.970.44999.1
2.55-2.646.6870.3277.749425740073910.9790.35499.9
2.64-2.746.0050.2678.3741399698468940.9770.29398.7
2.74-2.857.0530.20210.9647763679467720.9880.21899.7
2.85-2.987.2180.16412.7847118654465280.990.17799.8
2.98-3.137.2130.13514.8944771620762070.9920.146100
3.13-3.37.1390.11316.5642155591159050.9930.12299.9
3.3-3.57.1170.09718.739792559155910.9940.105100
3.5-3.747.060.08620.2337228527352730.9950.093100
3.74-4.046.8260.07921.4533138485548550.9940.086100
4.04-4.426.5440.07521.9729712454445400.9950.08199.9
4.42-4.945.8060.0721.2723005407039620.9940.07797.3
4.94-5.717.3710.0724.0426609361036100.9960.076100
5.71-6.997.5590.06824.5322958303730370.9950.072100
6.99-9.897.5470.05825.7217645233823380.9970.063100
9.89-48.337.260.05925.789271128712770.9950.06499.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7TCR

7tcr


Resolution: 2.21→48.33 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 1997 3.37 %
Rwork0.183 57276 -
obs0.1842 59273 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.49 Å2 / Biso mean: 39.7504 Å2 / Biso min: 22.88 Å2
Refinement stepCycle: final / Resolution: 2.21→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7442 0 16 343 7801
Biso mean--51.04 39.38 -
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 (%)
2.21-2.270.31891300.28633710384091
2.27-2.330.33751390.24113991413098
2.33-2.40.27041420.219140964238100
2.4-2.470.28061410.21244029417099
2.47-2.560.32221430.21554075421899
2.56-2.660.26421410.2284083422499
2.66-2.790.26861410.21234043418499
2.79-2.930.23991440.204641154259100
2.93-3.120.27681420.209441034245100
3.12-3.360.24221460.210841554301100
3.36-3.690.22291440.180941494293100
3.69-4.230.18221470.154441924339100
4.23-5.330.16981440.14014127427198
5.33-48.330.16741530.154844084561100
Refinement TLS params.Method: refined / Origin x: 11.027 Å / Origin y: 2.5139 Å / Origin z: 81.4539 Å
111213212223313233
T0.2206 Å2-0.0473 Å20.0112 Å2-0.3189 Å2-0.0067 Å2--0.2762 Å2
L0.2568 °2-0.466 °20.0118 °2-1.4076 °20.2027 °2--0.3238 °2
S-0.0191 Å °0.0141 Å °0.0338 Å °0.0611 Å °-0.0121 Å °0.0359 Å °-0.0326 Å °0.0069 Å °0.0278 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 - 375
7X-RAY DIFFRACTION1allG1 - 2

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more