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- PDB-8hkr: Crystal Structure of Histone H3 Lysine 79 (H3K79) Methyltransfera... -

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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 type 12 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: _ / 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: _ / Auth seq-ID: 18 - 405 / Label seq-ID: 21 - 408

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

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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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SAH / 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


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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

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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

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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

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