[English] 日本語
Yorodumi
- PDB-8h26: Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h26
TitleCrystal structure of MnmM from S. aureus complexed with SAH (1.50 A)
Components16S rRNA (Cytosine(1402)-N(4))-methyltransferase
KeywordsTRANSFERASE / Methyltrnasferase tRNA post-transcriptional modification MnmC mnm5(s2)U
Function / homologytRNA 5-(aminomethyl)-2-thiouridylate-methyltransferase / Putative rRNA methylase / Putative rRNA methylase / tRNA processing / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / tRNA (mnm(5)s(2)U34)-methyltransferase
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, J. / Cho, G. / Lee, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A)
Authors: Kim, J. / Cho, G. / Lee, J.
History
DepositionOct 5, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
B: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
C: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
D: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
E: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
F: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,32710
Polymers131,7906
Non-polymers1,5384
Water12,214678
1
A: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
E: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3143
Polymers43,9302
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-12 kcal/mol
Surface area15050 Å2
MethodPISA
2
B: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
C: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6994
Polymers43,9302
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-12 kcal/mol
Surface area15710 Å2
MethodPISA
3
D: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
F: 16S rRNA (Cytosine(1402)-N(4))-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3143
Polymers43,9302
Non-polymers3841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-14 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.329, 69.362, 74.608
Angle α, β, γ (deg.)91.25, 112.97, 114.05
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
16S rRNA (Cytosine(1402)-N(4))-methyltransferase


Mass: 21964.928 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_01878 / Plasmid: pLATE31 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FXG9
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS pH 6.5 and 25% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→67.09 Å / Num. obs: 104221 / % possible obs: 92.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 14.7
Reflection shellResolution: 1.5→1.68 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.285 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5203 / CC1/2: 0.637 / Rpim(I) all: 0.507 / Rrim(I) all: 1.382 / % possible all: 72.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MxDCdata collection
XDSJan 10, 2022data reduction
STARANISOdata scaling
Coot0.9.8.3model building
MOLREP11.9.02phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold model (UniProt: Q2FXG9)

Resolution: 1.5→67.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.95 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21855 5112 4.9 %RANDOM
Rwork0.18281 ---
obs0.18451 98695 63.35 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.04 Å20.02 Å2
2--0.51 Å20.01 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.5→67.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8298 0 104 678 9080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0188705
X-RAY DIFFRACTIONr_bond_other_d0.0020.028253
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.86511808
X-RAY DIFFRACTIONr_angle_other_deg1.2072.81219050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64151062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24224.953430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.909151528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3721518
X-RAY DIFFRACTIONr_chiral_restr0.1180.21371
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021847
X-RAY DIFFRACTIONr_mcbond_it2.1321.5054263
X-RAY DIFFRACTIONr_mcbond_other2.131.5054263
X-RAY DIFFRACTIONr_mcangle_it3.1492.2335320
X-RAY DIFFRACTIONr_mcangle_other3.152.2345321
X-RAY DIFFRACTIONr_scbond_it2.9421.9024442
X-RAY DIFFRACTIONr_scbond_other2.9421.9024442
X-RAY DIFFRACTIONr_scangle_other4.4812.7256489
X-RAY DIFFRACTIONr_long_range_B_refined7.0520.0739594
X-RAY DIFFRACTIONr_long_range_B_other7.01319.5199439
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 16 -
Rwork0.297 230 -
obs--2.03 %
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)
12.496-0.89350.71162.58550.43961.733-0.11670.02390.2865-0.07920.0741-0.0786-0.380.10790.04260.0902-0.0291-0.00630.0140.00910.1109-23.67-12.28919.363
22.4468-1.0547-0.14022.9863-0.0291.77020.04310.12110.0164-0.229-0.09480.04350.0138-0.08780.05170.0360.0138-0.02130.0149-0.01330.047-11.0621.761-1.387
31.7543-0.32050.20383.62430.24681.38890.0417-0.0051-0.0635-0.2151-0.0675-0.10570.01960.06510.02580.01630.00590.01430.00520.00490.04964.464-6.1843.311
41.732-0.220.3543.652-0.50861.9541-0.0574-0.01110.05880.1930.04740.1667-0.233-0.15480.010.08060.05380.01030.03860.0030.017119.2235.267-24.411
52.02140.41380.65633.31480.83411.92380.1579-0.1533-0.23040.3691-0.0062-0.20950.28590.05-0.15170.06860.0011-0.04780.01820.01030.0694-15.446-42.7723.861
61.3103-0.75370.09653.89630.21661.2964-0.0027-0.0141-0.1510.22030.0722-0.09770.0909-0.0855-0.06950.04720.0076-0.03860.0347-0.00910.076929.0565.086-22.865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 187
2X-RAY DIFFRACTION2B1 - 187
3X-RAY DIFFRACTION3C1 - 188
4X-RAY DIFFRACTION4D1 - 188
5X-RAY DIFFRACTION5E1 - 189
6X-RAY DIFFRACTION6F1 - 187

+
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