PDB-8qdi: compound 1b bound KMT9 crystal structure

ID or keywords:

Entry

Database: PDB / ID: 8qdi

Title

compound 1b bound KMT9 crystal structure

Components

Methyltransferase N6AMT1
Multifunctional methyltransferase subunit TRM112-like protein

Keywords

TRANSFERASE / Protein transferase / gene regulation

Function / homology

Function and homology information

arsonoacetate metabolic process / arsenite methyltransferase activity / protein-glutamine N-methyltransferase activity / eRF1 methyltransferase complex / peptidyl-glutamine methylation / tRNA (m2G10) methyltransferase complex / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / histone H4K12 methyltransferase activity / toxin metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.467 Å

Authors

Sheng, W. / Eric, M. / Roland, S.

Funding support

Germany, 5items

Organization	Grant number	Country
German Research Foundation (DFG)	SFB1381	Germany
German Research Foundation (DFG)	SFB992	Germany
German Research Foundation (DFG)	Schu688	Germany
German Research Foundation (DFG)	EXC-2189	Germany
German Research Foundation (DFG)	DKTK FR01-374	Germany

Citation

Journal: To Be Published
Title: compound 1a bound KMT9 crystal structure
Authors: Sheng, W. / Eric, M. / Roland, S.

History

Deposition	Aug 29, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 11, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8qdi.cif.gz	344.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8qdi.ent.gz	215.3 KB	Display	PDB format
PDBx/mmJSON format	8qdi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8qdi_validation.pdf.gz	740.4 KB	Display	wwPDB validaton report
Full document	8qdi_full_validation.pdf.gz	744 KB	Display
Data in XML	8qdi_validation.xml.gz	17.8 KB	Display
Data in CIF	8qdi_validation.cif.gz	24.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qd/8qdi ftp://data.pdbj.org/pub/pdb/validation_reports/qd/8qdi	HTTPS FTP

-
Related structure data

Related structure data	8qdgC 9fimC 9fkeC 9fkgC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#60 - Dec 2004 Ubiquitin similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Methyltransferase N6AMT1

B: Multifunctional methyltransferase subunit TRM112-like protein

hetero molecules

36.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	110.516, 110.516, 129.837
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22

Components on special symmetry positions

ID	Model	Components
1	1	B-277- HOH

#1: Protein	Methyltransferase N6AMT1 / HemK methyltransferase family member 2 / M.HsaHemK2P / Lysine N-methyltransferase 9 / ...HemK methyltransferase family member 2 / M.HsaHemK2P / Lysine N-methyltransferase 9 / Methylarsonite methyltransferase N6AMT1 / Protein N(5)-glutamine methyltransferase Mass: 21804.064 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: N6AMT1, C21orf127, HEMK2, KMT9, PRED28 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y5N5, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein	Multifunctional methyltransferase subunit TRM112-like protein / tRNA methyltransferase 112 homolog Mass: 14272.412 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRMT112, AD-001, HSPC152, HSPC170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UI30
#3: Chemical	ChemComp-QII / (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[2-[(2~{R})-pyrrolidin-2-yl]ethyl]amino]-2-azanyl-butanoic acid Mass: 464.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₀H₃₂N₈O₅ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.17 Å³/Da / Density % sol: 61.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.1 M Na3Citrate, 0.1M HEPES 7.25

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X06DA / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 12, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.467→47.901 Å / Num. obs: 80097 / % possible obs: 99.8 % / Redundancy: 39.4 % / CC_1/2: 1 / R_merge(I) obs: 0.095 / R_pim(I) all: 0.021 / R_rim(I) all: 0.097 / Net I/σ(I): 26.4

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
8.03-47.85	34.3	0.031	606	1	0.007	0.031
1.47-1.49	29.6	4.189	3793	0.448	1.086	4.331

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.467→47.901 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.965 / SU B: 2.045 / SU ML: 0.034 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1905	4033	5.039 %
R_work	0.1576	75996	-
all	0.159	-	-
obs	-	80029	99.782 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 24.636 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.3 Å²	-0.15 Å²	-0 Å²
2-	-	-0.3 Å²	0 Å²
3-	-	-	0.975 Å²

Refinement step

Cycle: LAST / Resolution: 1.467→47.901 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2407	0	33	184	2624

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.012	2570
X-RAY DIFFRACTION	r_bond_other_d	0.008	0.016	2438
X-RAY DIFFRACTION	r_angle_refined_deg	1.736	1.646	3510
X-RAY DIFFRACTION	r_angle_other_deg	0.606	1.551	5711
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.639	5	335
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.481	5	17
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.381	10	444
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.154	10	105
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	410
X-RAY DIFFRACTION	r_chiral_restr_other	0.044	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2915
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	468
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	406
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	2194
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	1235
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	1354
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.121	0.2	127
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.15	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.177	0.2	77
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.162	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	6.123	2.236	1283
X-RAY DIFFRACTION	r_mcbond_other	6.114	2.235	1283
X-RAY DIFFRACTION	r_mcangle_it	6.649	3.346	1610
X-RAY DIFFRACTION	r_mcangle_other	6.652	3.348	1611
X-RAY DIFFRACTION	r_scbond_it	10.385	2.826	1287
X-RAY DIFFRACTION	r_scbond_other	10.381	2.826	1288
X-RAY DIFFRACTION	r_scangle_it	10.284	3.986	1891
X-RAY DIFFRACTION	r_scangle_other	10.281	3.987	1892
X-RAY DIFFRACTION	r_lrange_it	8.838	31.212	2698
X-RAY DIFFRACTION	r_lrange_other	8.843	30.329	2668
X-RAY DIFFRACTION	r_rigid_bond_restr	13.962	3	5008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.467-1.505	0.383	272	0.355	5409	0.356	5824	0.949	0.947	97.5446	0.352
1.505-1.546	0.374	317	0.313	5385	0.316	5702	0.95	0.969	100	0.305
1.546-1.591	0.286	271	0.252	5257	0.253	5528	0.967	0.979	100	0.24
1.591-1.64	0.237	307	0.202	5093	0.204	5400	0.975	0.985	100	0.187
1.64-1.693	0.2	230	0.169	4979	0.171	5209	0.979	0.987	100	0.151
1.693-1.753	0.185	240	0.139	4830	0.141	5070	0.982	0.989	100	0.12
1.753-1.819	0.168	234	0.121	4636	0.123	4870	0.982	0.991	100	0.104
1.819-1.893	0.176	242	0.121	4472	0.124	4716	0.984	0.992	99.9576	0.107
1.893-1.977	0.188	227	0.133	4319	0.136	4546	0.98	0.991	100	0.121
1.977-2.073	0.164	230	0.139	4086	0.14	4316	0.986	0.992	100	0.129
2.073-2.185	0.177	198	0.145	3941	0.146	4139	0.985	0.991	100	0.136
2.185-2.318	0.165	188	0.139	3736	0.141	3924	0.983	0.991	100	0.13
2.318-2.477	0.176	201	0.137	3499	0.139	3700	0.981	0.99	100	0.127
2.477-2.675	0.167	182	0.142	3259	0.143	3444	0.983	0.988	99.9129	0.132
2.675-2.929	0.187	170	0.153	3041	0.155	3211	0.98	0.986	100	0.143
2.929-3.274	0.204	143	0.169	2766	0.17	2909	0.971	0.982	100	0.162
3.274-3.777	0.144	129	0.143	2464	0.143	2593	0.986	0.988	100	0.143
3.777-4.619	0.17	113	0.131	2123	0.133	2236	0.983	0.99	100	0.137
4.619-6.502	0.227	85	0.189	1680	0.191	1767	0.979	0.985	99.8868	0.199
6.502-47.901	0.26	54	0.213	1021	0.215	1075	0.964	0.976	100	0.228

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.0149	-0.0157	0.0005	0.0518	0.0337	0.0334	0.0014	-0.0014	-0.0031	-0.0016	-0.0015	0.0034	0.0005	-0.0026	0.0001	0.0108	-0.0011	0.0008	0.011	0.0001	0.0012	-42.4116	-6.9182	-16.5154
2	0.0202	0.0027	-0.0098	0.008	0.0114	0.0262	0.001	0.001	0.0011	0	-0.0007	0.0003	-0.0013	-0.002	-0.0003	0.0105	0.0003	-0.0002	0.01	0.0002	0.0001	-47.3507	-26.8381	-2.4533

Refinement TLS group

Selection: ALL

-
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

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi