[English] 日本語
Yorodumi
- PDB-8hkr: Crystal Structure of Histone H3 Lysine 79 (H3K79) Methyltransfera... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hkr
TitleCrystal Structure of Histone H3 Lysine 79 (H3K79) Methyltransferase Rv2067c from Mycobacterium tuberculosis
ComponentsProtein lysine methyltransferase
KeywordsTRANSFERASE / Mycobacterium tuberculosis / SAM-binding / Class I methyltransferase / Dimerization domain
Function / homologyMethyltransferase domain / Methyltransferase domain / peptidoglycan-based cell wall / methyltransferase activity / S-adenosyl-L-methionine-dependent methyltransferase superfamily / plasma membrane / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein Rv2067c
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsDadireddy, V. / Singh, P.R. / Kalladi, S.M. / Valakunja, N. / Ramakumar, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)CRG/2019/000077 India
CitationJournal: Nat Commun / Year: 2023
Title: The Mycobacterium tuberculosis methyltransferase Rv2067c manipulates host epigenetic programming to promote its own survival.
Authors: Singh, P.R. / Dadireddy, V. / Udupa, S. / Kalladi, S.M. / Shee, S. / Khosla, S. / Rajmani, R.S. / Singh, A. / Ramakumar, S. / Nagaraja, V.
History
DepositionNov 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _entity.pdbx_description / _struct_keywords.pdbx_keywords / _struct_keywords.text

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein lysine methyltransferase
B: Protein lysine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3926
Polymers92,4332
Non-polymers9594
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-39 kcal/mol
Surface area32200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.150, 109.150, 216.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 18 - 405 / Label seq-ID: 21 - 408

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Protein lysine methyltransferase


Mass: 46216.645 Da / Num. of mol.: 2 / Mutation: M1V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618/H37Rv / Gene: Rv2067c, MTCY49.06c / Plasmid: pMyNT
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WLL9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.49 Å3/Da / Density % sol: 64.75 % / Description: Rod shape
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Buffer: 0.1 M imidazole/MES acid, pH 6.5: Precipitant: 20% w/v polyethylene glycol 500* monomethyl ether + 10% w/v polyethylene glycol 20,000: Additive: 0.03 M sodium nitrate + 0.03 M sodium ...Details: Buffer: 0.1 M imidazole/MES acid, pH 6.5: Precipitant: 20% w/v polyethylene glycol 500* monomethyl ether + 10% w/v polyethylene glycol 20,000: Additive: 0.03 M sodium nitrate + 0.03 M sodium phosphate dibasic + 0.03 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.699996 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.699996 Å / Relative weight: 1
ReflectionResolution: 2.4→48.81 Å / Num. obs: 51986 / % possible obs: 100 % / Redundancy: 25.383 % / Biso Wilson estimate: 71.257 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.09 / Χ2: 0.863 / Net I/σ(I): 24.37 / Num. measured all: 1319560 / Scaling rejects: 56
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
2.4-2.4625.6332.2231.7196971378437830.7412.268100
2.46-2.5324.9061.7822.1592002369436940.8321.819100
2.53-2.624.6721.2593.0488327358035800.9061.286100
2.6-2.6826.6140.9664.1991924345534540.9410.985100
2.68-2.7726.4490.6695.9190245341234120.9660.682100
2.77-2.8725.9530.4818.0585332328832880.9830.49100
2.87-2.9824.8110.37610.0478404316031600.9860.384100
2.98-3.125.1870.27913.0476769304830480.9940.285100
3.1-3.2426.790.19319.0779004295029490.9970.196100
3.24-3.3926.5720.13526.4774454280228020.9980.137100
3.39-3.5826.0790.10133.8569839267826780.9990.103100
3.58-3.7924.080.0840.1361333254725470.9990.082100
3.79-4.0625.5140.06847.8961437240824080.9990.07100
4.06-4.3826.0850.05855.4658508224322430.9990.059100
4.38-4.825.2350.05259.9852236207020700.9990.054100
4.8-5.3723.5540.05257.4344353188318830.9990.053100
5.37-6.224.2710.05556.3141164169616960.9990.056100
6.2-7.5925.0190.04963.24362531449144910.05100
7.59-10.7322.1880.04267.7325605115411540.9990.043100
10.73-48.8122.3840.03870.47154006986880.9990.03998.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-1.93-39.962-7.667I105.40.96
2-17.899-23.195-39.964I109.850.96
3-13.975-23.849-59.886I126.780.96
4-14.111-43.886-85.322I119.550.96
54.329-51.32-89.293I111.590.87
6-27.179-14.695-44.57I126.390.88
71.051-58.321-78.298I124.890.96
8-5.734-39.3572.069I125.130.88
9-6.535-32.62122.271I147.710.75
10-36.266-51.227-58.889I142.310.66
1113.171-32.2-6.654I130.160.61
124.94-29.42332.942I175.10.82
13-4.272-65.974-89.737I131.620.62
1411.239-31.691-21.222I111.740.38
15-20.845-71.255-87.698I168.910.8
167.748-17.0562.969I114.380.3
1714.039-23.8526.294I148.840.52
1883.31821.9619.375I128.450.6
1960.54116.90223.422I163.340.47
2054.95423.04543.281I79.20.31
2155.30518.54349.334I82.650.35
22101.22844.85832.992I100.080.39
2364.09142.9126.803I124.30.41
2444.6354.54128.099I93.020.3
2596.47517.16418.082I74.90.26
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.54 Å48.81 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEJan 10, 2022 BUILT=20220820data scaling
PHASER2.8.3phasing
CRANK22.0.253phasing
PDB_EXTRACT3.27data extraction
XDS1.12data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Determined using iodine SAD; experimental phasing

Resolution: 2.4→48.81 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 14.771 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2600 5 %RANDOM
Rwork0.2017 ---
obs0.2025 49385 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.34 Å2 / Biso mean: 66.041 Å2 / Biso min: 47.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å2-0 Å2
2--0.5 Å2-0 Å2
3----1 Å2
Refinement stepCycle: final / Resolution: 2.4→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6068 0 62 54 6184
Biso mean--76.99 58.14 -
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0136298
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155858
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.6388581
X-RAY DIFFRACTIONr_angle_other_deg1.191.57513423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.27920.603348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8515974
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4141554
X-RAY DIFFRACTIONr_chiral_restr0.0590.2794
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021533
X-RAY DIFFRACTIONr_mcbond_it1.774.743049
X-RAY DIFFRACTIONr_mcbond_other1.774.743049
X-RAY DIFFRACTIONr_mcangle_it2.7677.1043799
Refine LS restraints NCS

Ens-ID: 1 / Number: 11978 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 189 -
Rwork0.333 3575 -
all-3764 -
obs--100 %
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)
11.08380.161-0.01921.5944-0.73411.21140.08880.1331-0.0508-0.1073-0.0210.06890.1615-0.1011-0.06770.1828-0.0417-0.02630.2079-0.01630.0098-4.790851.02689.3611
22.3296-0.8550.22751.0880.06750.63450.01780.10050.1263-0.2774-0.06150.0679-0.0919-0.05550.04360.23510.0153-0.01860.20980.02420.0572-28.115981.636464.2428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 502
2X-RAY DIFFRACTION2B18 - 502

+
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