PDB-2nyu: Crystal Structure of Human FtsJ homolog 2 (E.coli) protein in com...

ID or keywords:

Entry

Database: PDB / ID: 2nyu

Title

Crystal Structure of Human FtsJ homolog 2 (E.coli) protein in complex with S-adenosylmethionine

Components

Putative ribosomal RNA methyltransferase 2

Keywords

TRANSFERASE / SAM / ribosomal RNA / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

rRNA modification in the mitochondrion / rRNA 2'-O-methylation / mitochondrial large ribosomal subunit assembly / rRNA (uridine-2'-O-)-methyltransferase activity / RNA methylation / rRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing / mitochondrial matrix / nucleolus / mitochondrion
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Dong, A. / Wu, H. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)

Citation

Journal: To be Published
Title: The Crystal Structure of Human FtsJ homolog 2 (E.coli) protein in complex with AdoMet
Authors: Wu, H. / Dong, A. / Zeng, H. / Loppnau, P. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.

History

Deposition	Nov 21, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 5, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2nyu.cif.gz	159.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2nyu.ent.gz	126.9 KB	Display	PDB format
PDBx/mmJSON format	2nyu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	2nyu_validation.pdf.gz	924.9 KB	Display	wwPDB validaton report
Full document	2nyu_full_validation.pdf.gz	933.6 KB	Display
Data in XML	2nyu_validation.xml.gz	18.1 KB	Display
Data in CIF	2nyu_validation.cif.gz	25.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ny/2nyu ftp://data.pdbj.org/pub/pdb/validation_reports/ny/2nyu	HTTPS FTP

-
Related structure data

Related structure data	1eizS S: Starting model for refinement
Similar structure data	4v1p-d 5n6o-2 3th5-1 1on4-d 3im5-2 2z0p-1 5zz3-d 5wje-d 3kkq-d 6fa3-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#103 - Jul 2008 Dengue Virus similarity (2) #197 - May 2016 Zika Virus similarity (2) #139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Putative ribosomal RNA methyltransferase 2

B: Putative ribosomal RNA methyltransferase 2

hetero molecules

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

1

A: Putative ribosomal RNA methyltransferase 2

hetero molecules

defined by author
22.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Putative ribosomal RNA methyltransferase 2

hetero molecules

defined by author
22.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.022, 102.022, 37.068
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	Putative ribosomal RNA methyltransferase 2 / rRNA (uridine-2'-O-)-methyltransferase Mass: 21710.846 Da / Num. of mol.: 2 / Fragment: Residues 51-246 / Mutation: C54S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FTSJ2, FJH1 / Plasmid: P28-LIC-THROMBIN DERIVED FROM PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon plus Ril References: UniProt: Q9UI43, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.6 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.2M Potassium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.76→50 Å / Num. all: 37711 / Num. obs: 37711 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / B_iso Wilson estimate: 33.2 Å² / R_merge(I) obs: 0.048 / R_sym value: 0.048 / Net I/σ(I): 16.2
Reflection shell	Resolution: 1.76→1.79 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.629 / Mean I/σ(I) obs: 1.65 / Num. unique all: 1860 / R_sym value: 0.629 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
JDirector		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1EIZ

1eiz

Resolution: 1.76→50 Å / Cor.coef. F_o:F_c: 0.942 / Cor.coef. F_o:F_c free: 0.912 / SU B: 5.854 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.142 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. COOT 0.1.2 HAS ALSO BEEN USED IN THE REFINEMENT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.28113	784	2.1 %	RANDOM
R_work	0.22639	-	-	-
all	0.22753	36889	-	-
obs	0.22753	36889	98.39 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 27.895 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.26 Å²	0 Å²	0 Å²
2-	-	-0.26 Å²	0 Å²
3-	-	-	0.51 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2787	0	54	201	3042

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	2906
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.473	1.994	3970
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.43	5	367
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.223	23.162	117
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.338	15	448
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.308	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	466
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2193
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	1326
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	2003
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	195
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.164	0.2	30
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.158	0.2	18
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.169	1.5	1898
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.715	2	2968
X-RAY DIFFRACTION	r_scbond_it	2.613	3	1149
X-RAY DIFFRACTION	r_scangle_it	3.649	4.5	1002
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.76→1.81 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.367	63	-
R_work	0.281	2705	-
obs	-	-	99.96 %

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	5.6233	-2.6809	0.9699	10.1728	2.4113	3.3271	-0.1298	-0.209	0.1868	0.6935	0.0887	-0.2994	0.1894	0.2761	0.0411	0.103	-0.0069	-0.0213	0.1148	0.0036	-0.0682	47.0076	18.134	24.3722
2	8.0399	-7.2798	3.8321	11.2029	-2.4042	10.9605	-0.4875	-0.2968	0.3968	0.8319	0.4263	-0.4338	-0.2912	0.3211	0.0612	0.0906	-0.0137	0.0361	0.0386	-0.0698	0.0325	38.5975	29.0016	23.9234
3	3.8575	-0.2467	0.4668	1.0448	0.2734	2.5163	0.0057	-0.0651	0.0746	0.148	-0.0552	0.1033	0.1819	-0.0586	0.0495	0.0753	-0.0118	0.0167	0.0531	-0.0196	0.025	39.0602	18.8026	16.2835
4	5.658	-0.194	-0.3103	1.8434	0.2416	1.7373	-0.0012	0.1111	-0.3877	0.068	-0.0083	0.1124	0.2572	-0.0202	0.0094	0.0988	-0.0094	0.0133	0.0519	-0.0345	0.0583	40.5169	12.4476	12.0872
5	5.3051	-0.5838	-2.1576	1.2513	0.4706	2.9786	-0.0286	0.592	-0.0786	-0.3506	-0.0122	0.1096	0.2102	0.206	0.0408	0.0705	0.0183	-0.0135	0.1985	-0.0067	-0.0639	40.9091	19.5907	0.8084
6	4.3433	1.6145	-0.6855	0.8171	-0.0649	0.2743	0.078	0.1557	0.1322	-0.0833	0.014	-0.1419	-0.0372	0.0445	-0.092	0.0158	0.0089	0.0267	0.0815	0.0058	0.073	51.7737	28.5349	8.7021
7	5.6283	3.8909	-1.4742	5.9181	-5.5026	6.6129	0.1334	-0.4944	0.316	0.1289	-0.2105	-0.1374	0.0709	0.3776	0.0772	-0.0615	-0.0537	0.1326	-0.0073	-0.117	0.4705	54.1274	36.4801	13.033
8	7.3484	-0.0309	0.0473	7.7185	3.551	11.0766	0.2769	0.5195	0.8932	-0.3654	0.1481	-0.6167	-0.2815	-0.0773	-0.425	-0.0004	-0.0048	0.0659	-0.0853	0.0585	0.261	41.6911	39.028	10.0761
9	33.5987	-11.1426	-7.4522	7.5135	-7.0343	29.0763	-0.9258	-2.5493	0.7789	1.2469	0.8204	-0.4121	0.3033	1.8229	0.1054	-0.097	-0.0198	-0.1377	0.2026	-0.0438	0.1642	50.4289	33.4078	22.1603
10	9.2447	-0.2362	3.6529	5.4025	0.7897	8.7681	-0.1206	0.2388	0.3554	-0.0093	0.0201	-0.3035	-0.3871	-0.0697	0.1005	0.0298	-0.0405	0.0331	-0.0035	0.0324	0.1742	40.5678	34.5148	11.9552
11	11.46	3.8165	2.8245	29.0478	5.8202	1.5534	-0.4459	1.356	0.8665	-1.2018	0.5892	-0.2009	-0.0924	0.225	-0.1433	0.1033	-0.014	0.0015	0.1165	0.0771	-0.0877	19.5539	30.1748	-4.4818
12	18.9916	3.1889	-0.5663	1.9424	0.6347	1.0732	-0.1197	0.9724	-0.4812	-0.4012	-0.0503	0.1401	-0.0483	0.1222	0.1701	0.0563	0.0635	-0.0583	0.1614	-0.0416	-0.0482	7.6559	25.1502	-5.8926
13	3.614	-0.8973	-0.2251	1.5218	-0.8233	0.703	0.0012	0.0991	0.3689	-0.1503	-0.036	0.1586	-0.0367	-0.0677	0.0349	0.0115	0.0443	-0.0639	0.0646	-0.0494	0.0801	10.081	32.7115	2.8057
14	6.4155	-1.8302	1.3463	1.3923	-1.4359	1.7628	-0.1535	-0.2043	1.1052	-0.0205	0.045	-0.2872	-0.1317	-0.1391	0.1085	0.0047	0.0408	-0.0623	0.0334	-0.0792	0.1694	15.8713	36.182	7.1998
15	20.8591	0.6042	-3.9707	14.9029	-1.1546	15.1942	0.2162	-1.4218	1.0514	1.0735	0.1111	0.739	0.4102	-0.6017	-0.3274	0.0037	-0.0295	0.0213	0.3439	-0.0902	-0.0741	16.4574	27.4564	20.516
16	6.7783	-2.5813	-0.7656	4.1585	0.865	0.432	-0.1334	-0.8374	0.2845	0.2572	0.0406	0.1819	0.0141	-0.2138	0.0928	-0.0251	0.0552	-0.0316	0.1982	-0.0977	0.0103	11.0296	28.4314	12.5606
17	5.5754	-3.819	-1.4799	4.7644	2.012	2.7263	0.1031	-0.4012	-0.0345	-0.0431	0.1344	-0.0516	0.184	-0.195	-0.2376	0.0358	-0.0288	-0.0472	0.0651	0.0662	0.0852	18.4598	12.13	10.2193
18	4.5118	-4.6399	-4.5445	7.8194	4.365	10.1542	-0.0588	-0.4391	-0.2682	0.373	-0.0508	0.2321	0.3783	-0.358	0.1096	-0.0677	-0.0132	-0.0189	0.2399	-0.0608	0.0771	5.6276	22.9242	10.802
19	3.019	-1.4453	2.0154	4.1218	0.2543	2.0986	0.0509	-0.2408	-0.518	-0.1978	0.0023	0.4347	0.5001	-0.2642	-0.0532	-0.0618	-0.0492	-0.1347	-0.0053	0.1091	0.2215	8.3268	9.9852	8.3585
20	8.2614	-1.9094	0.6126	5.5098	3.1172	7.1114	0.2719	-0.1534	-0.5371	-0.2102	-0.1147	0.0371	0.1195	-0.1052	-0.1572	-0.0489	0.0144	-0.0734	0.0645	-0.0006	0.1253	3.597	17.4146	3.9683

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 11	1 - 11
2	X-RAY DIFFRACTION	2	A	A	12 - 19	12 - 19
3	X-RAY DIFFRACTION	3	A	A	20 - 45	20 - 45
4	X-RAY DIFFRACTION	4	A	A	46 - 79	46 - 79
5	X-RAY DIFFRACTION	5	A	A	80 - 100	80 - 100
6	X-RAY DIFFRACTION	6	A	A	101 - 142	101 - 142
7	X-RAY DIFFRACTION	7	A	A	143 - 155	143 - 155
8	X-RAY DIFFRACTION	8	A	A	156 - 166	156 - 166
9	X-RAY DIFFRACTION	9	A	A	167 - 180	167 - 180
10	X-RAY DIFFRACTION	10	A	A	181 - 189	181 - 189
11	X-RAY DIFFRACTION	11	B	B	1 - 6	1 - 6
12	X-RAY DIFFRACTION	12	B	B	7 - 18	7 - 18
13	X-RAY DIFFRACTION	13	B	B	19 - 47	19 - 47
14	X-RAY DIFFRACTION	14	B	B	48 - 79	48 - 79
15	X-RAY DIFFRACTION	15	B	B	80 - 89	80 - 89
16	X-RAY DIFFRACTION	16	B	B	90 - 108	90 - 108
17	X-RAY DIFFRACTION	17	B	B	109 - 131	109 - 131
18	X-RAY DIFFRACTION	18	B	B	132 - 145	132 - 145
19	X-RAY DIFFRACTION	19	B	B	146 - 161	146 - 161
20	X-RAY DIFFRACTION	20	B	B	162 - 189	162 - 189

-
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://pdbjlvh1.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