PDB-7y7n: Crystal structure of DUF371 domain-containing protein from Methan...

ID or keywords:

Entry

Database: PDB / ID: 7y7n

Title

Crystal structure of DUF371 domain-containing protein from Methanobrevibacter ruminantium

Components

Uncharacterized protein

Keywords

STRUCTURAL GENOMICS / unknow function

Function / homology

Protein of unknown function DUF371 / Mth639-like domain superfamily / Domain of unknown function (DUF371) / DUF371 domain-containing protein

Function and homology information

Biological species

Methanobrevibacter ruminantium (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.764 Å

Authors

Yang, Q. / Lai, Z.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of DUF371 domain-containing protein from methanobrevibacter ruminantium
Authors: Yang, Q. / Lai, Z.

History

Deposition	Jun 22, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 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	7y7n.cif.gz	67.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7y7n.ent.gz	47.2 KB	Display	PDB format
PDBx/mmJSON format	7y7n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y7/7y7n ftp://data.pdbj.org/pub/pdb/validation_reports/y7/7y7n	HTTPS FTP

-
Related structure data

Related structure data	3cbnS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	47.354, 47.354, 135.877
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-251- HOH

#1: Protein	Uncharacterized protein Mass: 15417.749 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanobrevibacter ruminantium (archaea) Strain: ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1 / Gene: mru_1462 / Production host: Escherichia (bacteria) / References: UniProt: D3E451
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.47 Å³/Da / Density % sol: 50.21 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 12.00% w/v Polyethylene glycol 8,000,5.00% w/v Glycerol,100 mM Potassium chloride

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97919 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 2, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97919 Å / Relative weight: 1
Reflection	Resolution: 1.76→44.72 Å / Num. obs: 16164 / % possible obs: 100 % / Redundancy: 9.3 % / CC_1/2: 0.999 / R_merge(I) obs: 0.09 / R_pim(I) all: 0.043 / R_rim(I) all: 0.1 / Net I/σ(I): 12.3
Reflection shell	Resolution: 1.76→1.79 Å / Redundancy: 9.8 % / R_merge(I) obs: 1.597 / Num. unique obs: 864 / CC_1/2: 0.837 / R_pim(I) all: 0.763 / R_rim(I) all: 0.098

-
Processing

Software

Name: REFMAC / Version: 5.8.0267 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3cbn

3cbn

Resolution: 1.764→44.716 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.921 / SU B: 3.099 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.13 / ESU R Free: 0.131
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2693	781	4.876 %
R_work	0.224	15235	-
all	0.226	-	-
obs	-	16016	99.919 %

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: 31.081 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.011 Å²	0 Å²	-0 Å²
2-	-	1.011 Å²	-0 Å²
3-	-	-	-2.022 Å²

Refinement step

Cycle: LAST / Resolution: 1.764→44.716 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1076	0	0	52	1128

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	1090
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1070
X-RAY DIFFRACTION	r_angle_refined_deg	1.729	1.629	1465
X-RAY DIFFRACTION	r_angle_other_deg	1.412	1.598	2491
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.39	5	136
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.028	25.102	49
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.188	15	220
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.934	15	3
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	152
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1187
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	203
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	168
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.18	0.2	1012
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	529
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	544
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	46
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.161	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.204	0.2	22
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.111	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	2.536	2.987	547
X-RAY DIFFRACTION	r_mcbond_other	2.531	2.987	546
X-RAY DIFFRACTION	r_mcangle_it	3.251	4.472	682
X-RAY DIFFRACTION	r_mcangle_other	3.249	4.472	683
X-RAY DIFFRACTION	r_scbond_it	4.03	3.504	543
X-RAY DIFFRACTION	r_scbond_other	4.03	3.504	543
X-RAY DIFFRACTION	r_scangle_it	6.078	5.037	783
X-RAY DIFFRACTION	r_scangle_other	6.074	5.036	784
X-RAY DIFFRACTION	r_lrange_it	7.192	35.848	1114
X-RAY DIFFRACTION	r_lrange_other	7.194	35.618	1105

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
1.764-1.809	0.364	50	0.278	1094	0.281	1148	0.793	0.837	99.6516	0.255
1.809-1.859	0.317	48	0.275	1073	0.277	1124	0.804	0.849	99.7331	0.251
1.859-1.913	0.285	66	0.251	1030	0.254	1096	0.877	0.878	100	0.22
1.913-1.972	0.258	55	0.242	1021	0.243	1076	0.886	0.896	100	0.218
1.972-2.036	0.259	43	0.235	965	0.236	1009	0.922	0.909	99.9009	0.214
2.036-2.107	0.224	47	0.223	959	0.223	1007	0.937	0.92	99.9007	0.202
2.107-2.187	0.284	51	0.231	913	0.233	964	0.921	0.926	100	0.209
2.187-2.276	0.346	37	0.229	905	0.233	942	0.85	0.912	100	0.21
2.276-2.377	0.326	51	0.239	859	0.243	910	0.87	0.899	100	0.219
2.377-2.492	0.24	27	0.219	835	0.22	862	0.929	0.933	100	0.206
2.492-2.627	0.305	52	0.223	782	0.228	835	0.925	0.933	99.8802	0.212
2.627-2.785	0.368	33	0.236	750	0.242	783	0.871	0.919	100	0.226
2.785-2.977	0.284	45	0.236	691	0.238	736	0.928	0.924	100	0.235
2.977-3.214	0.228	32	0.218	663	0.219	695	0.937	0.94	100	0.228
3.214-3.519	0.2	25	0.213	620	0.213	645	0.954	0.95	100	0.237
3.519-3.932	0.157	27	0.188	572	0.186	599	0.969	0.964	100	0.217
3.932-4.534	0.227	29	0.19	489	0.192	519	0.951	0.966	99.8073	0.228
4.534-5.539	0.317	26	0.201	439	0.206	465	0.935	0.966	100	0.262
5.539-7.774	0.257	22	0.274	350	0.273	372	0.941	0.932	100	0.337
7.774-44.716	0.402	14	0.268	225	0.276	241	0.893	0.935	99.1701	0.351

-
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