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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tcr
TitleMethanobactin biosynthetic protein complex of MbnB and MbnC from Methylosinus trichosporium OB3b at 2.62 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 / SAD / Resolution: 2.62 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 1.2Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
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)107,83914
Polymers107,1204
Non-polymers71910
Water1,02757
1
A: Methanobactin biosynthesis cassette protein MbnB
D: Methanobactin biosynthesis cassette protein MbnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9207
Polymers53,5602
Non-polymers3605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-100 kcal/mol
Surface area19140 Å2
MethodPISA
2
B: Methanobactin biosynthesis cassette protein MbnB
C: Methanobactin biosynthesis cassette protein MbnC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9207
Polymers53,5602
Non-polymers3605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-101 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.780, 215.640, 214.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
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.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.76 Å3/Da / Density % sol: 49.98 % / Description: yellow colored long plate
Crystal growTemperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M lithium sulfate, 0.1 M HEPES, pH 7, Bis-Tris, pH 6.5, 25% 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: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.722 Å / Relative weight: 1
ReflectionResolution: 2.62→48.5 Å / Num. obs: 35237 / % possible obs: 99.26 % / Redundancy: 23.1 % / Biso Wilson estimate: 54.56 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.02517 / Rrim(I) all: 0.1268 / Net I/σ(I): 26.12
Reflection shellResolution: 2.62→2.714 Å / Redundancy: 23 % / Rmerge(I) obs: 0.8037 / Mean I/σ(I) obs: 5.47 / Num. unique obs: 3396 / CC1/2: 0.976 / CC star: 0.994 / Rpim(I) all: 0.1693 / Rrim(I) all: 0.8218 / % possible all: 99.12

-
Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.62→48.5 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8855
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2374 2000 5.68 %
Rwork0.2036 33237 -
obs0.2056 35237 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.97 Å2
Refinement stepCycle: LAST / Resolution: 2.62→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7434 0 26 57 7517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00287652
X-RAY DIFFRACTIONf_angle_d0.566310394
X-RAY DIFFRACTIONf_chiral_restr0.04061108
X-RAY DIFFRACTIONf_plane_restr0.00391350
X-RAY DIFFRACTIONf_dihedral_angle_d4.73891016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.680.44411360.40412251X-RAY DIFFRACTION96.8
2.68-2.750.46261410.34642351X-RAY DIFFRACTION99.12
2.75-2.830.33751400.30572313X-RAY DIFFRACTION98.47
2.83-2.930.3391390.26582327X-RAY DIFFRACTION97.28
2.93-3.030.28441400.24972316X-RAY DIFFRACTION99.76
3.03-3.150.27051440.23852388X-RAY DIFFRACTION99.88
3.15-3.290.27951430.24162382X-RAY DIFFRACTION100
3.29-3.470.28821420.24612360X-RAY DIFFRACTION100
3.47-3.690.20861430.20292387X-RAY DIFFRACTION99.96
3.69-3.970.21751440.16982387X-RAY DIFFRACTION99.96
3.97-4.370.22071440.17082399X-RAY DIFFRACTION99.26
4.37-50.18641460.15672411X-RAY DIFFRACTION98.88
5-6.30.19681440.18282397X-RAY DIFFRACTION98.3
6.3-48.50.19121540.16772568X-RAY DIFFRACTION99.85
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.252596490920.1020523969680.8992664965762.99863282813-0.9044018243093.54403871613-0.174283251264-0.08401480727810.6303390137970.15899880029-0.2364942326640.0563443159897-1.365497596340.1894803268770.1035313632830.976880690407-0.0804275111455-0.1322991877710.4501220422630.009858083508130.5474200243179.9845666225739.121811470393.2932000042
21.3625052629-2.06552457970.973972699177.78446598096-5.33199232213.84404710342-0.6996804871320.5059412041080.544722833470.02224630116270.259261933033-0.797288417753-0.718056984754-0.05266771042010.4289961312620.865198848759-0.205516018032-0.07999260167420.799640836884-0.005457852131040.67073178465318.740693150928.358188938392.1462997311
34.333272802341.3630236278-0.8623808291856.035172517-3.18932094558.63147865441-0.0668020754322-0.1585977276920.008616325078180.4956135116840.353285317502-0.594981352164-1.06732713787-0.180591923334-0.1979993215710.34958390803-0.0747785272035-0.009552710751080.572247255448-0.01894883899370.43563468443418.38742513920.298139398987.5818018504
44.895832121890.809835141318-0.000565286823375.39941169244-3.502026663083.081021820180.2262446313810.394298956234-0.1287210765780.268427536043-0.654070756614-1.57663122532-0.4799025491571.441955955730.4326804829770.546252863406-0.18481904844-0.0342232015980.7370115465420.04000070884140.81118077153126.822046471222.409149139484.8781139788
53.57683394550.4176160283190.5048878260574.787666060130.9294072612866.192135355770.05934784025040.501247726194-0.138425243248-0.425373902571-0.1360045029780.418265384920.404361393217-0.3665857356870.07929985876050.3817657417180.0488963907058-0.05616214135670.489790742663-0.0453173922160.4694094500225.42552623353-12.847534997272.142142126
63.26447607368-0.03830933866620.5915737463793.84235467290.560807825195.548147288140.3126020203460.5684898740070.187680424399-0.757562741051-0.260733882199-0.1850747368510.02404669284350.133468418056-0.05557300181040.4010992225380.06819866443640.03886364374460.456305759592-0.02576256999260.4121405671518.6712676028-9.6498098617773.0690367294
79.00294774176-0.1063248450771.220285162364.60881942871-1.448288017815.793005048580.0259735986910.2350870486320.552238432069-0.585384262662-0.0991211957181-0.671243403962-0.2003513308720.2247781511660.1168911343320.3723104313180.00153005885380.1487319576830.389402644845-0.0772665117210.55099515043525.9599457282-3.9088696882673.6085166199
81.86335545284-0.33468180056-0.8531419045533.376317914180.06215528611443.07113247919-0.0267163014284-0.1773473464790.06871689803450.3940505944590.169586309994-0.1073384914840.2059721011780.143942065575-0.141142959220.2669159783610.0519060440715-0.02407588732870.352293297737-0.03894729579670.35053972006317.3919657275-14.232468857391.7800320637
92.1240804157-2.71318967431-0.6086150364757.71712821570.6993836028620.230841185346-0.03325731396970.271524034351-0.559804334848-0.06380489842710.0348660296531.307639041540.299154841491-0.02410095804980.05529853808430.391601518145-0.05324138596530.06361569696010.5411799299340.006247043173920.5963847068891.8157398305-17.271222375690.0767931294
105.291768418811.10523889157-1.424983010678.745239268633.188766713857.76152386987-0.005987688867220.0273822803304-0.0148717026173-0.513605179942-0.3421380751380.8461174970470.255795201392-0.2371952437340.2829314896710.2792200978480.0298773500516-0.09959600529070.49069416003-0.05910150099660.623776016012-0.637423053157-17.205837515379.4121981017
114.64109917871-0.81310726823-1.640251747862.395734942281.824099786335.09791991006-0.280046952105-0.493131364485-0.3826635893460.8222952986350.2067282037170.04757303706940.5973226011710.6876001354280.04018734251020.6023491366580.1034938967130.004612944989790.3982728138370.02112490331890.41614930123922.7595292921-34.162228395993.5190001462
122.741937673590.316106632862-0.926392615347.10027771723-1.300305469134.24123891722-0.0179032570932-0.0844911064741-0.085236725598-0.1817863589910.0538064002424-0.4406383405960.3813547997660.13857719165-0.05701584048570.3454562934120.09347241702750.0139703017820.435267502627-0.01716971070070.44648590980730.1055549199-38.333322339773.1266182885
133.0112370546-0.8156619364170.7236592234641.376354341860.05376162536326.032630959530.106715643236-0.1440428324410.255735218813-0.2028442532560.0690932885431-0.165509018378-0.1396485667970.472279806896-0.1896283202650.3440759261810.005620486836210.06870710671840.447032066512-0.006095384699280.41719564571532.5372552933-24.031990914161.2115356664
142.14700726727-0.7242576070130.573332182043.08807585292-2.336977110475.51335350331-0.116231883698-0.4619898997470.2658593027810.707015845341-0.05760954182480.369070947635-0.897423923654-0.3657283370720.170714541950.7294010521780.04627639334880.04806033666580.440560052625-0.08813980438860.516472548032-3.4817361960239.639239291993.7242157065
152.949110948391.28563097307-0.2406086231643.623803360051.907533517643.683861283720.0655260541148-0.03787414451450.205448976168-0.277213396526-0.1419087578020.413694324033-0.445288962119-0.2628325650410.03567828298440.5131481628370.0803757133624-0.1404429117850.381081200123-0.008371311113480.459205576806-8.0497000073743.109688063472.3658235615
164.25241727349-1.27583413655-1.075806613562.18510499491-1.138231160045.91388410401-0.1019933461030.208872009906-0.257675944209-0.208495580862-0.07956984307930.4191631443820.0447601156142-0.2405619938030.1898495923440.6011469161980.0284884230862-0.2065608776710.423067175971-0.09212174368490.556262602664-8.372302261428.498402470460.5050967993
174.35190321301-0.811558106591.871355685982.74618615143-0.7274663765965.96290349433-0.05150524829320.421764900129-0.0958667587105-0.3674385074110.0139586814509-0.386626783623-0.6580139680380.5693612084890.09688976125060.506597092933-0.03094900636550.0879377030410.4901293973140.01183214734910.48358529432215.062326025517.572439785873.0478476032
183.15733272879-0.862932572105-0.4389767416234.025728365061.034869484323.57454799266-0.0107763987705-0.101817912556-0.182512954892-0.0994305134182-0.1152200621120.451588115172-0.131740833864-0.3032291831590.1654423447820.296475768042-0.00835408003483-0.04146777417070.2973449892970.03056588654920.385862364625-2.1621921371115.808665310483.2210647459
192.093015187981.166554068070.824615838965.682781712790.6128693720292.65726849314-0.0208036087294-0.126519056939-0.06405769525850.5528238245570.0795489788535-0.0248306924572-0.48706423532-0.0930038179911-0.03098435593190.3841858267810.02684429717340.0190747491560.412507127190.07010383672740.3251115277933.410604767720.456984334494.4291896912
202.19250333308-0.1060276448780.4563328411694.214586768430.9746781326743.42475044799-0.0874168941505-0.230532785727-0.02702702810990.6726533940880.147136881551-0.0280339148043-0.1986433010340.240435271808-0.04793661198410.455655286331-0.0271748718177-0.06130809870030.4076615070850.03249002352670.347468899338.555468759817.811859920197.2468877971
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 195 through 207 )AA195 - 207195 - 207
22chain 'A' and (resid 208 through 224 )AA208 - 224208 - 224
33chain 'A' and (resid 225 through 245 )AA225 - 245225 - 245
44chain 'A' and (resid 246 through 263 )AA246 - 263246 - 263
55chain 'B' and (resid 1 through 34 )BB1 - 341 - 34
66chain 'B' and (resid 35 through 64 )BB35 - 6435 - 64
77chain 'B' and (resid 65 through 82 )BB65 - 8265 - 82
88chain 'B' and (resid 83 through 204 )BB83 - 20483 - 204
99chain 'B' and (resid 205 through 234 )BB205 - 234205 - 234
1010chain 'B' and (resid 235 through 263 )BB235 - 263235 - 263
1111chain 'C' and (resid 2 through 50 )CC2 - 501 - 49
1212chain 'C' and (resid 51 through 122 )CC51 - 12250 - 121
1313chain 'C' and (resid 123 through 195 )CC123 - 195122 - 194
1414chain 'D' and (resid 2 through 50 )DD2 - 501 - 49
1515chain 'D' and (resid 51 through 122 )DD51 - 12250 - 121
1616chain 'D' and (resid 123 through 195 )DD123 - 195122 - 194
1717chain 'A' and (resid 1 through 46 )AA1 - 461 - 46
1818chain 'A' and (resid 47 through 126 )AA47 - 12647 - 126
1919chain 'A' and (resid 127 through 144 )AA127 - 144127 - 144
2020chain 'A' and (resid 145 through 194 )AA145 - 194145 - 194

+
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