PDB-6nz6: YcjX-GDP (type II)

ID or keywords:

Entry

Database: PDB / ID: 6nz6

Title

YcjX-GDP (type II)

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 /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Tsai, J. / Sung, N. / Lee, J. / Chang, C. / Lee, S. / 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	6nz6.cif.gz	385 KB	Display	PDBx/mmCIF format
PDB format	pdb6nz6.ent.gz	314.7 KB	Display	PDB format
PDBx/mmJSON format	6nz6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6nz6_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6nz6_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6nz6_validation.xml.gz	39 KB	Display
Data in CIF	6nz6_validation.cif.gz	57.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nz/6nz6 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/6nz6	HTTPS FTP

-
Related structure data

Related structure data	6nz4C 6nz5C C: citing same article (ref.)
Similar structure data	6nz5-d 6nz4-d 6ujy-d 6glz-d 6gm1-d 6uir-d 6anq-2 5zok-d 6o0e-2 6q2t-d 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)	59.385, 134.100, 145.024
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 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.: 619 / 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: 2.65 Å³/Da / Density % sol: 53.6 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 50mM Na Cacodylate pH 6.5, 50mM MES pH 6.0, 27.5%(v/v) PEP426

-
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: Aug 18, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.95→50 Å / Num. obs: 78678 / % possible obs: 92.2 % / Redundancy: 5.8 % / Net I/σ(I): 41
Reflection shell	Resolution: 1.95→1.98 Å

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→45.944 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.78

	R_factor	Num. reflection	% reflection
R_free	0.2046	3030	2.74 %
R_work	0.1621	-	-
obs	0.1633	110527	67.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→45.944 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7131	0	56	619	7806

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7459
X-RAY DIFFRACTION	f_angle_d	0.672	10151
X-RAY DIFFRACTION	f_dihedral_angle_d	14.752	4430
X-RAY DIFFRACTION	f_chiral_restr	0.044	1116
X-RAY DIFFRACTION	f_plane_restr	0.004	1314

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 (%)
1.95-1.9805	0.2878	39	0.2478	1652	X-RAY DIFFRACTION	23
1.9805-2.013	0.315	49	0.2222	1876	X-RAY DIFFRACTION	26
2.013-2.0477	0.2417	63	0.2164	2153	X-RAY DIFFRACTION	30
2.0477-2.0849	0.3071	71	0.2193	2313	X-RAY DIFFRACTION	32
2.0849-2.125	0.2286	67	0.2015	2590	X-RAY DIFFRACTION	35
2.125-2.1684	0.2505	78	0.2002	2785	X-RAY DIFFRACTION	39
2.1684-2.2155	0.2268	92	0.1932	3144	X-RAY DIFFRACTION	43
2.2155-2.2671	0.2333	94	0.1761	3518	X-RAY DIFFRACTION	49
2.2671-2.3238	0.211	117	0.172	3805	X-RAY DIFFRACTION	53
2.3238-2.3866	0.2421	131	0.1753	4669	X-RAY DIFFRACTION	65
2.3866-2.4568	0.2023	135	0.168	5181	X-RAY DIFFRACTION	72
2.4568-2.5361	0.2295	173	0.1765	5585	X-RAY DIFFRACTION	78
2.5361-2.6267	0.2177	171	0.1798	5893	X-RAY DIFFRACTION	82
2.6267-2.7319	0.2179	169	0.1807	6189	X-RAY DIFFRACTION	86
2.7319-2.8562	0.2253	182	0.1768	6369	X-RAY DIFFRACTION	88
2.8562-3.0068	0.214	184	0.1812	6874	X-RAY DIFFRACTION	95
3.0068-3.1951	0.2083	212	0.1791	7096	X-RAY DIFFRACTION	98
3.1951-3.4417	0.217	192	0.1649	7208	X-RAY DIFFRACTION	100
3.4417-3.788	0.185	222	0.143	7085	X-RAY DIFFRACTION	99
3.788-4.3357	0.1875	204	0.1356	7216	X-RAY DIFFRACTION	100
4.3357-5.4611	0.1659	188	0.1287	7140	X-RAY DIFFRACTION	99
5.4611-45.9565	0.1796	197	0.1478	7156	X-RAY DIFFRACTION	99

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	1.5151	0.0287	-0.2705	0.3466	0.3377	1.2734	-0.018	0.4737	-0.225	-0.1705	0.0671	-0.1214	-0.0221	0.381	-0.028	0.0194	0.0291	0.0211	0.2354	-0.046	0.1239	40.7646	90.9838	10.9249
2	0.8198	0.4675	-0.2824	1.411	0.0936	0.7944	0.0471	-0.1056	-0.3095	0.1444	-0.0148	0.136	0.139	0.1397	0.0249	0.1251	0.0438	-0.0461	0.0583	0.0474	0.2532	34.5676	82.2618	24.3926
3	0.8042	0.1431	0.2053	0.6854	-0.0973	1.2637	0.0132	-0.2556	0.2765	0.2231	0.0344	0.0665	-0.1067	-0.0662	-0.0538	0.1206	0.0101	-0.002	0.0845	-0.0266	0.0899	24.941	100.2156	36.3802
4	0.4651	-0.1607	-0.1532	0.2799	-0.0414	1.3435	0.1098	-0.0663	0.2757	0.0561	-0.0453	-0.0197	-0.4881	0.0759	0.0674	0.0921	0.0051	0.0036	0.0463	-0.0346	0.118	27.4989	103.2899	27.0829
5	4.237	-0.6736	0.9751	3.2693	0.4864	4.7622	0.0669	0.1383	0.349	0.0884	0.1086	-0.0775	-0.5114	0.0349	0.1174	0.1544	0.0814	-0.0028	0.1636	0.0575	0.1409	20.235	104.5315	11.7029
6	1.4391	1.1345	0.1864	1.7997	0.4239	0.6429	-0.0317	0.4118	-0.2115	-0.3261	-0.08	0.2099	0.0815	-0.2587	0.0417	0.1545	0.0347	-0.0511	0.2497	-0.154	0.2545	16.2092	84.5043	5.6713
7	0.9711	-0.3454	0.1591	0.8645	-0.243	0.5056	0.0516	0.163	-0.134	-0.0307	-0.0301	0.216	0.0609	-0.3008	-0.0571	0.0465	0.0014	-0.0356	0.2586	-0.0666	0.2892	8.4209	92.621	12.4381
8	1.2412	-0.6254	0.3201	3.0206	0.2913	1.6339	0.0641	0.2582	-0.3725	-0.229	-0.1278	-0.098	0.0527	0.2084	0.0853	0.0652	0.0549	0.0155	0.1586	-0.0344	0.1607	35.1069	87.9521	8.3866
9	0.5845	-0.0263	0.21	0.0268	-0.122	0.6583	-0.0618	-0.6233	-0.1091	0.216	0.1375	0.11	-0.072	-0.2695	0.0732	0.2988	-0.0122	-0.0274	0.4857	0.1445	0.1275	31.664	87.8088	69.3471
10	0.8356	-0.2199	-0.1325	1.4624	-0.6137	1.1156	0.0561	-0.2024	-0.2772	-0.1957	0.1749	0.367	0.0741	-0.2166	-0.1526	0.2337	-0.0429	-0.1296	0.2251	0.1114	0.2138	26.2572	84.8534	54.8513
11	0.5088	0.0606	-0.2858	0.4205	0.0713	1.6193	-0.0727	-0.4796	0.102	0.1839	0.1331	-0.1407	-0.0635	0.0243	-0.099	0.2608	0.0406	-0.0864	0.345	-0.0085	0.098	39.3015	92.2379	64.697
12	1.1204	-0.396	-0.3052	0.9509	-0.0519	1.3778	0.0627	0.1531	-0.676	-0.0995	-0.0477	0.0367	0.5331	-0.0534	0.0412	0.3501	0.0827	-0.0388	0.1779	-0.0145	0.3757	48.4613	72.4638	37.098
13	0.9608	-0.0316	-0.3467	1.0746	0.1652	1.8265	0.1814	-0.0492	-0.2304	-0.1758	-0.1345	-0.2708	-0.0331	0.3681	-0.0079	0.1657	0.0674	-0.0188	0.1847	0.0344	0.1809	54.0396	82.7761	41.003
14	0.3239	0.6742	-0.4868	4.1063	0.5072	1.8647	-0.053	-0.2977	-0.3485	-0.0686	0.0955	-0.3997	0.1072	0.3923	0.0733	0.211	0.0083	-0.0684	0.2899	0.1358	0.2979	50.8302	77.924	58.0687
15	0.3443	-0.2014	0.1629	0.2355	-0.037	0.1071	0.0386	-0.2337	-0.2635	0.0988	0.0006	0.0342	0.232	-0.0058	0.1447	0.3069	-0.0033	-0.0518	0.4066	0.458	0.3685	40.7829	70.0257	69.5937
16	0.0999	0.0386	-0.172	1.0393	-0.7505	1.0766	-0.0156	-0.0314	-0.0169	0.0839	-0.075	-0.151	-0.1044	0.2085	0.2995	0.2119	-0.0492	-0.0337	0.5088	0.3335	0.3489	39.6667	70.5219	71.1323
17	0.3296	0.3581	-0.328	0.9956	-0.6617	1.0718	0.0222	-0.0367	-0.0607	-0.1661	0.0439	0.0576	0.2252	-0.0989	0.1005	0.3779	-0.0351	-0.059	0.4823	0.3928	0.6534	31.0691	59.9729	68.4611
18	1.1041	0.041	-0.1022	1.8503	-0.1302	1.4177	-0.0501	-0.4409	-0.4292	0.1192	0.1864	0.2882	0.2753	-0.1624	-0.1364	0.276	-0.0257	-0.0297	0.4476	0.232	0.3034	31.296	74.8466	68.0319

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 84 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 85 through 117 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118 through 268 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 269 through 360 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 361 through 387 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 388 through 427 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 428 through 456 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 457 through 485 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 24 through 84 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 85 through 117 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 118 through 163 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 164 through 245 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 246 through 304 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 305 through 347 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 348 through 376 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 377 through 409 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 410 through 438 )
18	X-RAY DIFFRACTION	18	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