PDB-6nz5: YcjX-GDPCP

ID or keywords:

Entry

Database: PDB / ID: 6nz5

Title

YcjX-GDPCP

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 / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / Ras-like GTPase YcjX

Function and homology information

Biological species

Shewanella oneidensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.233 Å

Authors

Lee, S. / Tsai, J. / Tsai, F.T. / Sung, N. / Lee, J. / Chang, C.

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

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PDBx/mmCIF format	6nz5.cif.gz	370.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6nz5.ent.gz	302.7 KB	Display	PDB format
PDBx/mmJSON format	6nz5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nz/6nz5 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/6nz5	HTTPS FTP

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Related structure data

Related structure data	6nz4C 6nz6C C: citing same article (ref.)
Similar structure data	6nz6-d 6nz4-d 5mep-d 2icx-d 6ujy-d 6anq-2 1rtd-1 3klg-1 1jrx-d 6glz-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

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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)	59.471, 128.257, 148.056
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: 54550.031 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-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₃P₃ / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.59 Å³/Da / Density % sol: 52.47 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100 mM HEPES pH 6.5 and 6% (w/v) polyvinyl pyrrolidone

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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: Oct 26, 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: 2.22→50 Å / Num. obs: 54859 / % possible obs: 98.6 % / Redundancy: 6.4 % / Net I/σ(I): 19
Reflection shell	Resolution: 2.22→2.26 Å

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Processing

Software

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

Refinement

Resolution: 2.233→46.363 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71

	R_factor	Num. reflection	% reflection
R_free	0.217	3179	4.2 %
R_work	0.1781	-	-
obs	0.1798	75767	71.33 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.233→46.363 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7123	0	60	282	7465

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7395
X-RAY DIFFRACTION	f_angle_d	0.577	10066
X-RAY DIFFRACTION	f_dihedral_angle_d	13.647	4372
X-RAY DIFFRACTION	f_chiral_restr	0.04	1113
X-RAY DIFFRACTION	f_plane_restr	0.003	1297

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 (%)
2.233-2.2664	0.2744	52	0.2553	1168	X-RAY DIFFRACTION	26
2.2664-2.3018	0.2873	55	0.2461	1302	X-RAY DIFFRACTION	29
2.3018-2.3395	0.2641	65	0.2377	1486	X-RAY DIFFRACTION	34
2.3395-2.3799	0.2864	72	0.2373	1664	X-RAY DIFFRACTION	37
2.3799-2.4231	0.2553	79	0.2368	1770	X-RAY DIFFRACTION	40
2.4231-2.4697	0.2821	88	0.236	2029	X-RAY DIFFRACTION	45
2.4697-2.5201	0.2649	94	0.2393	2197	X-RAY DIFFRACTION	50
2.5201-2.5749	0.252	118	0.2267	2496	X-RAY DIFFRACTION	56
2.5749-2.6348	0.2689	117	0.2331	2666	X-RAY DIFFRACTION	61
2.6348-2.7007	0.3091	132	0.2357	2969	X-RAY DIFFRACTION	67
2.7007-2.7737	0.268	140	0.2251	3028	X-RAY DIFFRACTION	69
2.7737-2.8553	0.2653	145	0.2217	3407	X-RAY DIFFRACTION	76
2.8553-2.9475	0.2778	166	0.2012	3808	X-RAY DIFFRACTION	86
2.9475-3.0528	0.2647	166	0.2047	3911	X-RAY DIFFRACTION	89
3.0528-3.175	0.2184	185	0.2087	4100	X-RAY DIFFRACTION	93
3.175-3.3195	0.2567	184	0.1948	4257	X-RAY DIFFRACTION	96
3.3195-3.4944	0.2061	184	0.1815	4323	X-RAY DIFFRACTION	97
3.4944-3.7133	0.2027	187	0.1723	4211	X-RAY DIFFRACTION	95
3.7133-3.9998	0.1965	192	0.167	4398	X-RAY DIFFRACTION	99
3.9998-4.4021	0.2044	186	0.1402	4350	X-RAY DIFFRACTION	99
4.4021-5.0384	0.1782	194	0.1256	4410	X-RAY DIFFRACTION	99
5.0384-6.3453	0.1851	190	0.1581	4288	X-RAY DIFFRACTION	97
6.3453-46.373	0.1588	188	0.1502	4350	X-RAY DIFFRACTION	98

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	0.0945	0.0063	-0.0412	0.009	0.0086	0.0803	0.0634	0.039	-0.0553	-0.0103	0.0349	-0.0237	0.0054	0.1236	0.0875	0.0015	-0.0257	-0.004	0.0864	-0.0333	0.137	38.0116	87.6418	13.5028
2	0.0194	0.0099	-0.004	0.0226	0.0143	0.0225	0.0554	0.0447	-0.1337	-0.0185	0.0205	0.0179	0.0077	0.0511	0.0437	0.079	0.0579	-0.055	0.2262	0.0612	0.1659	40.8488	82.6719	16.7509
3	0.0213	-0.0203	0.0152	0.0154	0.0003	0.0332	0.0305	-0.0182	-0.0802	0.0286	0.0315	0.0197	0.0177	0.0729	0.0654	0.0391	-0.0306	0.0045	0.1334	0.0678	0.1245	40.7856	83.2129	14.033
4	0.0579	-0.003	0.0397	0.015	-0.001	0.0222	-0.0705	-0.044	0.0189	0.12	0.0531	0.0729	-0.0874	-0.0813	-0.0241	0.0504	0.1033	0.217	0.1949	-0.008	-0.1162	19.8382	99.7258	38.0926
5	0.0107	-0.0097	0.0009	0.0212	-0.0041	0.0075	0.0181	-0.0494	-0.0341	0.0953	0.129	0.1	-0.0247	-0.0932	0.0936	0.1669	0.0226	0.0286	0.2363	0.0728	0.1361	18.8604	92.2697	41.2738
6	0.1227	-0.0244	0.052	0.1706	-0.0796	0.1299	-0.0788	-0.0256	0.0199	0.1388	0.0976	0.1246	-0.2137	-0.005	0.1455	0.1317	0.0434	-0.0267	0.0856	0.005	0.1045	24.4611	101.7882	32.119
7	0.0082	-0.0027	-0.0016	0.0073	-0.0072	0.0109	0.0261	0.0123	-0.0021	0.0177	0.0159	0.0112	-0.028	-0.0041	0.058	0.1135	0.0626	-0.0459	0.0704	-0.0265	0.1621	19.3368	101.2854	12.4735
8	0.0027	0.0114	0.0095	0.0304	0.0147	0.0076	0.0302	0.0608	-0.0562	-0.0487	-0.0344	0.0576	0.0205	-0.0428	0.0089	0.0365	-0.0585	-0.0951	0.0682	-0.1214	0.1865	15.1022	80.5939	6.2972
9	0.0165	0.0077	0.0072	0.0119	0.0044	0.034	0.0243	-0.0048	-0.0512	-0.0018	0.0192	0.005	0.0329	-0.0582	0.0317	0.0963	-0.0427	-0.0568	0.1965	-0.049	0.3058	7.3421	88.7391	13.4845
10	0.0041	0.0049	0.0012	0.029	0.0059	0.0251	0.0285	0.022	-0.0999	-0.0188	-0.0082	0.041	0.0066	0.0366	0.0191	0.0151	0.0378	-0.0111	0.1322	0.0187	0.1363	33.7921	83.8246	9.3538
11	0.0138	-0.0047	0.0042	0.0145	-0.0155	0.024	-0.008	-0.0975	-0.0397	-0.0006	0.0728	0.0737	-0.0419	-0.0586	0.0417	0.2469	0.0129	0.0866	0.1967	0.1857	0.1182	30.6716	86.0994	70.4321
12	0.012	-0.0104	0.0146	0.0352	-0.0103	0.0398	-0.0483	-0.0969	-0.0176	-0.0138	0.0303	0.0234	-0.0412	-0.0099	-0.057	0.3381	-0.0259	-0.0403	0.2174	0.1045	0.1076	33.4212	87.4099	61.1009
13	0.0513	-0.0299	0.0009	0.0143	0.0001	-0.0043	-0.073	0.0328	-0.1091	-0.0524	-0.0755	0.0195	0.1423	0.0857	-0.1645	0.1584	0.4627	0.1268	-0.0022	0.0011	0.1556	48.3287	70.0087	38.7268
14	0.0051	0.0147	-0.0065	0.0586	0.0106	0.076	0.117	0.003	-0.0366	0.0238	-0.1745	-0.0716	0.0136	0.162	0.0461	0.2175	0.0736	0.0745	0.2991	0.1538	0.1146	53.764	80.9375	41.3531
15	-0.0024	-0.0007	0.0014	0.0231	0.0309	0.0676	-0.0334	-0.0582	-0.1415	0.0049	0.0435	0.0467	-0.0042	0.1504	0.0901	0.135	-0.0504	0.109	0.1864	0.3869	0.1738	46.9164	73.727	63.7483
16	0.0616	0.0068	-0.0284	0.0292	-0.01	0.0633	0.03	-0.0257	-0.0052	-0.0264	0.0119	0.0145	0.0053	0.0446	0.0767	0.2718	-0.0239	0.0886	0.3778	0.228	0.3067	47.1181	76.1607	68.7419
17	0.0257	0.0121	0.0098	0.0319	0.0004	0.029	0.0056	-0.0028	-0.0012	-0.0141	0.0229	-0.0068	0.0156	0.0008	0.0304	0.2188	-0.1206	0.0366	0.3079	0.2451	0.4664	26.7867	57.2887	73.9439
18	0.0023	0.0102	-0.0093	0.0204	-0.028	0.0272	-0.0625	-0.0892	-0.1137	-0.0041	0.0241	0.0854	0.0526	0.0162	-0.0519	0.2335	0.0091	0.0571	0.3013	0.2088	0.2923	33.5785	71.6106	69.2247

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 103 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 104 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 201 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 202 through 245 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 246 through 360 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 361 through 387 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 388 through 427 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 428 through 456 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 457 through 485 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 24 through 84 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 85 through 163 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 164 through 245 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 246 through 303 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 304 through 376 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 377 through 399 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 400 through 432 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 433 through 485 )

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