[English] 日本語
Yorodumi
- PDB-7nkg: Methyl-coenzyme M reductase from Methermicoccus shengliensis at 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nkg
TitleMethyl-coenzyme M reductase from Methermicoccus shengliensis at 1.6-A resolution
Components(Methyl-coenzyme M reductase ...) x 3
KeywordsTRANSFERASE / Methyl-coenzyme M reductase / cofactor F430 / post-translational modification / archaea / methoxydotrophy / methanogenesis / coenzyme M / coenzyme B / heterodisulfide / radical mechanism / thermophile / thioglycine
Function / homology1-THIOETHANESULFONIC ACID / FACTOR 430 / : / Coenzyme B
Function and homology information
Biological speciesMethermicoccus shengliensis DSM 18856 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMueller, M. / Wagner, T.
Funding support Germany, Netherlands, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
Netherlands Organisation for Scientific Research (NWO)Gravitation grant 024.002.002 Netherlands
German Research Foundation (DFG)3768/1-1 Germany
CitationJournal: Microorganisms / Year: 2021
Title: Structural Insights into the Methane-Generating Enzyme from a Methoxydotrophic Methanogen Reveal a Restrained Gallery of Post-Translational Modifications.
Authors: Kurth, J.M. / Muller, M.C. / Welte, C.U. / Wagner, T.
History
DepositionFeb 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyl-coenzyme M reductase alpha subunit
B: Methyl-coenzyme M reductase beta subunit
C: Methyl-coenzyme M reductase gamma subunit
D: Methyl-coenzyme M reductase alpha subunit
E: Methyl-coenzyme M reductase beta subunit
F: Methyl-coenzyme M reductase gamma subunit
G: Methyl-coenzyme M reductase alpha subunit
H: Methyl-coenzyme M reductase beta subunit
I: Methyl-coenzyme M reductase gamma subunit
J: Methyl-coenzyme M reductase alpha subunit
K: Methyl-coenzyme M reductase beta subunit
L: Methyl-coenzyme M reductase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)551,71634
Polymers545,31212
Non-polymers6,40322
Water77,4284298
1
A: Methyl-coenzyme M reductase alpha subunit
B: Methyl-coenzyme M reductase beta subunit
C: Methyl-coenzyme M reductase gamma subunit
D: Methyl-coenzyme M reductase alpha subunit
E: Methyl-coenzyme M reductase beta subunit
F: Methyl-coenzyme M reductase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,04419
Polymers272,6566
Non-polymers3,38813
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
G: Methyl-coenzyme M reductase alpha subunit
H: Methyl-coenzyme M reductase beta subunit
I: Methyl-coenzyme M reductase gamma subunit
J: Methyl-coenzyme M reductase alpha subunit
K: Methyl-coenzyme M reductase beta subunit
L: Methyl-coenzyme M reductase gamma subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,67215
Polymers272,6566
Non-polymers3,0159
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.615, 148.177, 235.415
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Methyl-coenzyme M reductase ... , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
Methyl-coenzyme M reductase alpha subunit


Mass: 62295.250 Da / Num. of mol.: 4 / Mutation: wild-type / Source method: isolated from a natural source
Details: The polypeptide contains three post-translational modifications: Methylhistidine-275 Methylarginine-289 Thioglycine-463
Source: (natural) Methermicoccus shengliensis DSM 18856 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: ZC-1 / Tissue: / / References: coenzyme-B sulfoethylthiotransferase
#2: Protein
Methyl-coenzyme M reductase beta subunit


Mass: 45908.246 Da / Num. of mol.: 4 / Mutation: wild-type / Source method: isolated from a natural source
Source: (natural) Methermicoccus shengliensis DSM 18856 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: ZC-1 / Tissue: / / References: coenzyme-B sulfoethylthiotransferase
#3: Protein
Methyl-coenzyme M reductase gamma subunit


Mass: 28124.594 Da / Num. of mol.: 4 / Mutation: wild-type / Source method: isolated from a natural source
Source: (natural) Methermicoccus shengliensis DSM 18856 (archaea)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Strain: ZC-1 / Tissue: / / References: coenzyme-B sulfoethylthiotransferase

-
Non-polymers , 7 types, 4320 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-COM / 1-THIOETHANESULFONIC ACID


Mass: 142.197 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O3S2
#7: Chemical
ChemComp-TP7 / Coenzyme B / 7-MERCAPTOHEPTANOYLTHREONINEPHOSPHATE


Mass: 343.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H22NO7PS
#8: Chemical
ChemComp-F43 / FACTOR 430


Mass: 906.580 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C42H51N6NiO13
#9: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 4298 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.12 %
Description: Yellow thick brick-shape crystals appeared within two weeks
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The protein sample was at 47 g/l in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol and 2 mM dithiothreitol. MCR crystals were obtained aerobically by using the sitting drop method on 96-Well MRC 2- ...Details: The protein sample was at 47 g/l in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol and 2 mM dithiothreitol. MCR crystals were obtained aerobically by using the sitting drop method on 96-Well MRC 2-Drop Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 ul of mother liquor; the crystallization drop contained a mixture of 0.6 ul protein sample and 0.6 ul of crystallization solution. The crystallization solution contained 25% w/v polyethylene glycol 3350, 100 mM Bis-Tris pH 5.5 and 200 mM lithium sulfate.
PH range: / / Temp details: /

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→49.41 Å / Num. obs: 602614 / % possible obs: 99.7 % / Redundancy: 4.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.051 / Rrim(I) all: 0.105 / Net I/σ(I): 8.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.216 / Mean I/σ(I) obs: 1 / Num. unique obs: 87124 / CC1/2: 0.356 / Rpim(I) all: 0.661 / Rrim(I) all: 1.388 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E6Y

1e6y


Resolution: 1.6→48.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.09 / SU Rfree Blow DPI: 0.083 / SU Rfree Cruickshank DPI: 0.081
Details: The last cycle of refinement was performed with hydrogens in riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 30001 4.98 %RANDOM
Rwork0.1725 ---
obs0.1734 602442 99.7 %-
Displacement parametersBiso max: 136.35 Å2 / Biso mean: 42.85 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.7622 Å20 Å20 Å2
2---3.8335 Å20 Å2
3---2.0712 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.6→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37962 0 405 4298 42665
Biso mean--27.38 39.25 -
Num. residues----4960
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d23283SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes12500HARMONIC5
X-RAY DIFFRACTIONt_it39274HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion5120SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact68074SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d76578HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg138068HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion16.45
LS refinement shellResolution: 1.6→1.61 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2451 614 5.1 %
Rwork0.2342 11435 -
all0.2347 12049 -
obs--99.01 %
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)
10.17560.0325-0.04610.2257-0.07020.2111-0.01670.0205-0.0085-0.0244-0.0116-0.05130.00440.02660.0283-0.09290.00380.0091-0.0660.0008-0.070510.371844.5076-41.4697
20.16610.0106-0.03480.2371-0.11040.2465-0.01530.0147-0.0571-0.02270.02480.06190.0632-0.0869-0.0095-0.0843-0.02080.009-0.0589-0.0075-0.052-19.623130.323-31.0902
30.19710.0495-0.13080.2768-0.1460.33870.0215-0.04260.06090.13120.00660.0418-0.1382-0.0437-0.0281-0.02330.02130.0213-0.0571-0.0084-0.0765-9.646570.5561-18.4394
40.17410.0085-0.02620.2795-0.11910.2525-0.006-0.0907-0.00490.1385-0.0155-0.034-0.07120.03230.0215-0.04590.0001-0.0042-0.03210.0061-0.09620.572943.40780.8147
50.29870.002-0.07190.3028-0.15130.4680.01770.08920.0737-0.00470.01110.0379-0.115-0.0818-0.0288-0.03670.0392-0.0387-0.0001-0.0717-0.002-2.458379.3797-51.7699
60.18410.004-0.08480.4411-0.04490.3168-0.0332-0.1007-0.10470.07760.0212-0.00750.071-0.00630.012-0.07730.0130.0284-0.07960.0424-0.0689-5.7569.4095-1.5113
70.8830.65270.58390.71770.4041.3292-0.4111-0.13160.4874-0.39940.00120.3239-0.6323-0.41530.40990.14390.1387-0.271-0.0165-0.05190.0285-58.146856.6962-84.6817
80.83660.48680.64390.74540.48791.3260.1062-0.435-0.01560.085-0.17540.00610.0894-0.5720.0692-0.1384-0.0496-0.01780.2336-0.0015-0.0874-56.292730.9526-61.7165
90.94540.83760.75751.46850.60891.2377-0.17550.2688-0.2126-0.42940.29-0.2464-0.10010.1708-0.11450.0261-0.06660.08550.0078-0.0789-0.0665-44.205523.6527-102.644
101.18960.68050.73510.72080.59311.4476-0.0973-0.14630.0211-0.146-0.08390.16020.0245-0.73490.1812-0.1151-0.1016-0.04120.3388-0.0376-0.073-77.491819.3823-93.8246
1100.16780.16570.16710.16740.4464-0.117-0.0690.0731-0.06980.00530.0194-0.0542-0.23940.1117-0.0978-0.0020.03460.0857-0.0013-0.0709-31.440940.1582-54.3664
121.55060.880.71031.24430.57541.439-0.54570.62750.0213-0.61090.4925-0.2757-0.69110.60740.05320.3805-0.252-0.01520.2478-0.0797-0.1151-23.755652.6899-101.72
131.73980.47910.49530.55610.39012.04330.1893-0.87580.13460.0887-0.38180.21790.2011-1.33050.1925-0.2513-0.34280.05651.315-0.1999-0.1561-93.6920.5721-62.8821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|568 A|601 - A|601 }A5 - 568
2X-RAY DIFFRACTION1{ A|5 - A|568 A|601 - A|601 }A601
3X-RAY DIFFRACTION2{ B|2 - B|433 }B2 - 433
4X-RAY DIFFRACTION3{ C|2 - C|248 }C2 - 248
5X-RAY DIFFRACTION4{ D|5 - D|569 }D5 - 569
6X-RAY DIFFRACTION5{ E|2 - E|433 E|501 - E|501 }E2 - 433
7X-RAY DIFFRACTION5{ E|2 - E|433 E|501 - E|501 }E501
8X-RAY DIFFRACTION6{ F|2 - F|248 }F2 - 248
9X-RAY DIFFRACTION7{ G|7 - G|568 }G7 - 568
10X-RAY DIFFRACTION8{ H|2 - H|433 }H2 - 433
11X-RAY DIFFRACTION9{ I|2 - I|248 }I2 - 248
12X-RAY DIFFRACTION10{ J|6 - J|568 }J6 - 568
13X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }A603 - 606
14X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }B501 - 502
15X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }E502 - 503
16X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }D601 - 602
17X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }G602 - 605
18X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }H501
19X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }K501
20X-RAY DIFFRACTION11{ A|603 - A|606 B|501 - B|502 E|502 - E|503 D|601 - D|602 G|602 - G|605 H|501 - H|501 K|501 - K|501 J|601 - J|602 }J601 - 602
21X-RAY DIFFRACTION12{ K|2 - K|433 }K2 - 433
22X-RAY DIFFRACTION13{ L|3 - L|248 }L3 - 248

+
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