PDB-6nz4: YcjX-GDP (type I)

ID or keywords:

Entry

Database: PDB / ID: 6nz4

Title

YcjX-GDP (type I)

Components

YcjX Stress Protein

Keywords

SIGNALING PROTEIN / G-protein

Function / homology

Protein of unknown function DUF463, YcjX-like protein / YcjX-like family, DUF463 / small monomeric GTPase / GDP binding / GTPase activity / GTP binding / GUANOSINE-5'-DIPHOSPHATE / Ras-like GTPase YcjX

Function and homology information

Biological species

Shewanella oneidensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.92 Å

Authors

Lee, S. / Tsai, J. / Tsai, F.T.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM111084	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P01-HD087157	United States
Welch Foundation	Q-1530	United States

Citation

Journal: J.Mol.Biol. / Year: 2019
Title: Crystal Structure of the YcjX Stress Protein Reveals a Ras-Like GTP-Binding Protein.
Authors: Tsai, J.T. / Sung, N. / Lee, J. / Chang, C. / Lee, S. / Tsai, F.T.F.

History

Deposition	Feb 12, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 18, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6nz4.cif.gz	380.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6nz4.ent.gz	310.3 KB	Display	PDB format
PDBx/mmJSON format	6nz4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6nz4_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6nz4_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6nz4_validation.xml.gz	40.1 KB	Display
Data in CIF	6nz4_validation.cif.gz	59.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nz/6nz4 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/6nz4	HTTPS FTP

-
Related structure data

Related structure data	6nz5C 6nz6C C: citing same article (ref.)
Similar structure data	6nz6-d 6nz5-d 6ujy-d 4jeu-d 3glb-d 1vhk-d 6uir-d 6glz-d 3klg-1 6mfr-1 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	#148 - Apr 2012 Ras Protein similarity (1) #245 - May 2020 Spliceosomes similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: YcjX Stress Protein

B: YcjX Stress Protein

hetero molecules

110 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)	59.314, 133.942, 144.620
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	YcjX Stress Protein Mass: 54457.980 Da / Num. of mol.: 2 / Mutation: F187L, D218G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria) Strain: MR-1 / Gene: ycjX, SO_1810 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EG04
#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.64 Å³/Da / Density % sol: 53.36 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50mM MES pH 6.0, 400mM Ammonium Chloride, 15% MEPEG 2K

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.92→50 Å / Num. obs: 88457 / % possible obs: 99.3 % / Redundancy: 6.1 % / Net I/σ(I): 28.3
Reflection shell	Resolution: 1.92→1.95 Å

-
Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Resolution: 1.92→45.859 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.04

	R_factor	Num. reflection	% reflection
R_free	0.2228	3225	2.49 %
R_work	0.1801	-	-
obs	0.1812	129342	75.08 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.92→45.859 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7152	0	56	679	7887

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7483
X-RAY DIFFRACTION	f_angle_d	0.664	10197
X-RAY DIFFRACTION	f_dihedral_angle_d	14.095	4447
X-RAY DIFFRACTION	f_chiral_restr	0.044	1131
X-RAY DIFFRACTION	f_plane_restr	0.004	1318

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.92-1.9398	0.3141	46	0.2763	1688	X-RAY DIFFRACTION	23
1.9398-1.9701	0.2638	52	0.2533	2195	X-RAY DIFFRACTION	30
1.9701-2.0024	0.3003	67	0.2471	2306	X-RAY DIFFRACTION	32
2.0024-2.037	0.2547	74	0.2253	2704	X-RAY DIFFRACTION	37
2.037-2.074	0.2621	74	0.2203	2962	X-RAY DIFFRACTION	41
2.074-2.1139	0.2415	91	0.2055	3444	X-RAY DIFFRACTION	47
2.1139-2.157	0.1868	90	0.2039	3926	X-RAY DIFFRACTION	54
2.157-2.2039	0.2211	124	0.2122	4505	X-RAY DIFFRACTION	62
2.2039-2.2552	0.2173	117	0.2028	5090	X-RAY DIFFRACTION	70
2.2552-2.3116	0.2725	153	0.1994	5593	X-RAY DIFFRACTION	77
2.3116-2.3741	0.2295	159	0.1993	6022	X-RAY DIFFRACTION	82
2.3741-2.444	0.1981	157	0.2014	6224	X-RAY DIFFRACTION	86
2.444-2.5228	0.2956	179	0.201	6775	X-RAY DIFFRACTION	93
2.5228-2.613	0.2445	175	0.2026	7062	X-RAY DIFFRACTION	96
2.613-2.7176	0.2724	189	0.1956	7214	X-RAY DIFFRACTION	99
2.7176-2.8413	0.2942	189	0.2026	7331	X-RAY DIFFRACTION	100
2.8413-2.991	0.2489	173	0.1981	7303	X-RAY DIFFRACTION	100
2.991-3.1784	0.2556	191	0.1876	7269	X-RAY DIFFRACTION	100
3.1784-3.4237	0.2241	186	0.1697	7295	X-RAY DIFFRACTION	100
3.4237-3.7681	0.1883	188	0.154	7289	X-RAY DIFFRACTION	100
3.7681-4.313	0.1688	184	0.1443	7325	X-RAY DIFFRACTION	100
4.313-5.4326	0.1879	177	0.1424	7312	X-RAY DIFFRACTION	100
5.4326-45.8726	0.1924	190	0.172	7283	X-RAY DIFFRACTION	100

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	0.0036	-0.0039	-0.0017	0.0035	-0.0011	0.0182	0.0136	0.0838	-0.0175	-0.0262	0.0039	-0.0116	0.0096	0.0911	0.0215	-0.0182	0.018	0.0045	0.0893	-0.0453	0.0528	39.9026	89.6508	11.9835
2	0.0463	-0.0322	0.0508	0.0569	-0.008	0.0725	0.024	0.0654	-0.0732	-0.0044	0.0332	0.0099	0.0213	0.0807	0.0857	0.0273	0.041	-0.0272	0.1174	0.0033	0.0495	42.2349	87.0573	15.4443
3	0.1637	0.0171	0.0488	0.165	-0.1272	0.2067	0.043	0.0062	0.0653	0.1001	0.011	0.0524	-0.1217	-0.06	0.042	0.0544	-0.0015	0.007	0.0601	0.0027	0.06	23.3044	102.962	33.3109
4	0.0245	-0.0263	-0.0057	0.0434	0.0154	0.0087	0.0501	0.1109	-0.0952	-0.051	-0.022	0.0779	0.0415	0.01	-0.0003	-0.0551	0.0204	-0.1087	0.1162	-0.0962	0.1182	19.9878	88.2865	9.2438
5	0.0657	-0.015	0.0124	0.0031	-0.0021	0.0024	0.0268	-0.0905	-0.0512	0.0045	0.0406	0.0477	0.0006	-0.0769	0.0743	0.161	-0.0825	-0.0573	0.2105	0.1694	0.1466	31.8622	87.6031	68.8291
6	-0.0004	-0.0005	-0.0005	0.0123	-0.0062	0.0179	0.0286	-0.0181	-0.0498	-0.0177	0.0166	0.0296	0.0123	-0.0221	0.068	0.1678	-0.0633	-0.1333	0.0848	0.0834	0.1329	26.9277	84.6122	54.2052
7	0.0552	-0.0205	0.0176	0.0335	-0.0285	0.0231	0.0092	-0.0993	-0.0302	0.0431	0.0298	0.0063	0.0084	-0.0337	0.0796	0.182	-0.0162	-0.1045	0.1437	0.0494	0.0753	40.126	92.1982	64.0738
8	0.0019	-0.0076	0.0001	0.014	-0.0053	0.0008	0.0462	0.0543	-0.0579	-0.0183	-0.0153	-0.0115	0.0525	0.0292	0.0096	0.279	0.2654	-0.147	0.0873	-0.0534	0.2285	50.1331	72.747	36.6686
9	0.082	-0.0268	0.0409	0.0187	-0.0081	0.0246	0.1096	0.043	-0.0953	-0.0221	-0.0617	-0.0097	0.068	0.0294	0.0938	0.1957	0.0351	-0.1189	0.0376	0.0835	0.1084	51.1642	79.8412	47.5926
10	0.0437	-0.0161	-0.0544	0.0452	0.0414	0.0901	0.0464	-0.0189	-0.0379	-0.0223	0.0417	0.0193	-0.0316	0.0223	0.0751	0.1949	-0.1017	-0.0812	0.194	0.1264	0.2292	49.0293	83.1684	62.0953
11	0.0002	-0.0004	0.0005	0.0027	0.0005	0.0011	0.011	0.0015	-0.0047	0.0111	0.0007	-0.0025	-0.0014	0.014	0.0408	0.2712	0.0015	-0.0888	0.2328	0.1983	0.3202	48.3085	70.7981	68.8267
12	0.0111	-0.006	-0.0134	0.0209	0.0042	0.0192	-0.0379	0.0119	0.0205	0.0102	0.0088	0.0163	0.0039	0.0201	-0.0242	0.2346	-0.0677	-0.0588	0.2611	0.2107	0.3173	31.9641	66.1917	74.0324
13	0.0001	0.0004	0	0.0054	-0.0046	0.0018	-0.0062	-0.0005	-0.0084	0.0101	-0.0209	0.0101	0.0156	-0.0112	-0	0.4097	-0.0383	-0.0507	0.3575	0.2054	0.4898	31.4614	59.6753	67.94
14	0.0039	0.0044	-0.0065	0.0022	-0.0052	0.0105	0.0016	-0.042	-0.0535	-0.0019	0.0115	0.0255	0.0016	0.0194	0.0014	0.1686	-0.0673	-0.0641	0.2559	0.192	0.2141	31.3819	74.386	67.2716

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 70 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 71 through 139 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 140 through 387 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 388 through 485 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 24 through 84 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 85 through 117 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 118 through 163 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 164 through 257 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 258 through 330 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 331 through 360 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 361 through 387 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 388 through 409 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 410 through 438 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 439 through 485 )

-
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