[English] 日本語
- PDB-7m6b: The Crystal Structure of Mcbe1 -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 7m6b
TitleThe Crystal Structure of Mcbe1
ComponentsSite-specific DNA-methyltransferase (adenine-specific)DNA methyltransferase
KeywordsTRANSFERASE / methyl transferase
Function / homology
Function and homology information

site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity
Similarity search - Function
Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / S-ADENOSYLMETHIONINE / Site-specific DNA-methyltransferase (adenine-specific)
Similarity search - Component
Biological speciesCaldicellulosiruptor bescii (bacteria)
AuthorsAlahuhta, P.M. / Lunin, V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: The Crystal Structure of Mcbe1
Authors: Alahuhta, P.M. / Lunin, V.V.
DepositionMar 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
B: Site-specific DNA-methyltransferase (adenine-specific)
A: Site-specific DNA-methyltransferase (adenine-specific)
hetero molecules

Theoretical massNumber of molelcules
Total (without water)68,9697
B: Site-specific DNA-methyltransferase (adenine-specific)
hetero molecules

Theoretical massNumber of molelcules
Total (without water)34,6143
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
A: Site-specific DNA-methyltransferase (adenine-specific)
hetero molecules

Theoretical massNumber of molelcules
Total (without water)34,3544
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.446, 73.750, 160.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111B1 - 266
211A1 - 266

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)


#1: Protein Site-specific DNA-methyltransferase (adenine-specific) / DNA methyltransferase

Mass: 33831.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320) (bacteria)
Strain: ATCC BAA-1888 / DSM 6725 / Z-1320 / Gene: Athe_2437 / Production host: Escherichia coli (E. coli)
References: UniProt: B9MNH4, site-specific DNA-methyltransferase (adenine-specific)
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine

Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine

Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol

Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

Experimental details


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

Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M Citric acid pH 4.0 and 1.0 M NaCl

Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5419 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 26, 2013 / Details: HELIOS MIRRORS
RadiationMonochromator: HELIOS MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.9→43.429 Å / Num. obs: 50187 / % possible obs: 100 % / Redundancy: 6.39 % / Rsym value: 0.0766 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.07 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 7031 / Rsym value: 0.5786 / % possible all: 99.9


PROTEUM PLUSdata scaling
PROTEUM PLUSdata collection
PROTEUM PLUSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DPM
Resolution: 1.9→43.429 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.506 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2436 2498 4.989 %
Rwork0.2057 47568 -
all0.208 --
obs-50066 99.858 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.451 Å20 Å20 Å2
2--1.69 Å2-0 Å2
3----1.239 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3928 0 88 393 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173908
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6495637
X-RAY DIFFRACTIONr_angle_other_deg1.3231.5838990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0795480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76522.768224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69115703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5951520
X-RAY DIFFRACTIONr_chiral_restr0.0750.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024676
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021021
X-RAY DIFFRACTIONr_nbd_refined0.2060.2867
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.23729
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21993
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2313
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1550.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.217
X-RAY DIFFRACTIONr_nbd_other0.2110.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.214
X-RAY DIFFRACTIONr_mcbond_it2.6522.9641938
X-RAY DIFFRACTIONr_mcbond_other2.6522.9641938
X-RAY DIFFRACTIONr_mcangle_it3.9264.4222412
X-RAY DIFFRACTIONr_mcangle_other3.9264.4232413
X-RAY DIFFRACTIONr_scbond_it3.2893.2822234
X-RAY DIFFRACTIONr_scbond_other3.2893.2822234
X-RAY DIFFRACTIONr_scangle_it5.1554.773225
X-RAY DIFFRACTIONr_scangle_other5.1544.7693226
X-RAY DIFFRACTIONr_lrange_it7.38434.6314918
X-RAY DIFFRACTIONr_lrange_other7.30134.2794831
X-RAY DIFFRACTIONr_ncsr_local_group_10.130.057465
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.129780.05007
12AX-RAY DIFFRACTIONLocal ncs0.129780.05007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3511800.3323463X-RAY DIFFRACTION99.8082
1.949-2.0030.3241790.3113398X-RAY DIFFRACTION99.9721
2.003-2.0610.3311530.2833299X-RAY DIFFRACTION99.9132
2.061-2.1240.3051740.2743170X-RAY DIFFRACTION99.9104
2.124-2.1940.291580.2493122X-RAY DIFFRACTION99.9086
2.194-2.2710.2581750.2293003X-RAY DIFFRACTION99.9685
2.271-2.3560.2731530.232865X-RAY DIFFRACTION99.8346
2.356-2.4520.2731330.2082831X-RAY DIFFRACTION99.798
2.452-2.5610.2671490.2122671X-RAY DIFFRACTION99.8937
2.561-2.6860.2751300.1922576X-RAY DIFFRACTION99.8524
2.686-2.8310.2191350.1862457X-RAY DIFFRACTION99.8075
2.831-3.0030.2341260.1842314X-RAY DIFFRACTION99.9181
3.003-3.210.2391160.1942208X-RAY DIFFRACTION99.914
3.21-3.4670.2411150.1852046X-RAY DIFFRACTION99.5853
3.467-3.7970.214870.1791894X-RAY DIFFRACTION99.7482
3.797-4.2440.18950.1591720X-RAY DIFFRACTION99.9449
4.244-4.8980.207860.151545X-RAY DIFFRACTION99.8775
4.898-5.9930.185740.1751311X-RAY DIFFRACTION100
5.993-8.4520.21500.2051049X-RAY DIFFRACTION100
8.452-43.4290.3300.256626X-RAY DIFFRACTION98.6466

About Yorodumi


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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search


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