PDB-2pmc: Crystal Structure of CheY-Mg(2+) in Complex with CheZ(C15) Peptid...

ID or keywords:

Entry

Database: PDB / ID: 2pmc

Title

Crystal Structure of CheY-Mg(2+) in Complex with CheZ(C15) Peptide solved from a P1 Crystal

Components

Chemotaxis protein cheY
Chemotaxis protein cheZ

Keywords

SIGNALING PROTEIN / CHEMOTAXIS / CHEY-CHEZ PEPTIDE COMPLEX

Function / homology

Function and homology information

archaeal or bacterial-type flagellum-dependent cell motility / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / regulation of chemotaxis / bacterial-type flagellum / phosphorelay signal transduction system / phosphoprotein phosphatase activity / chemotaxis / metal ion binding / cytoplasm
Similarity search - Function

Biological species

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.688 Å

Authors

Guhaniyogi, J. / Stock, A.M.

Citation

Journal: J.Bacteriol. / Year: 2008
Title: Interaction of CheY with the C-terminal peptide of CheZ.
Authors: Guhaniyogi, J. / Wu, T. / Patel, S.S. / Stock, A.M.

History

Deposition	Apr 20, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 18, 2017	Group: Refinement description / Category: software
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2pmc.cif.gz	110.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2pmc.ent.gz	87.4 KB	Display	PDB format
PDBx/mmJSON format	2pmc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2pmc_validation.pdf.gz	462.7 KB	Display	wwPDB validaton report
Full document	2pmc_full_validation.pdf.gz	468.1 KB	Display
Data in XML	2pmc_validation.xml.gz	19.8 KB	Display
Data in CIF	2pmc_validation.cif.gz	27 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pm/2pmc ftp://data.pdbj.org/pub/pdb/validation_reports/pm/2pmc	HTTPS FTP

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Related structure data

Related structure data	2pl9C C: citing same article (ref.)
Similar structure data	5lbk-1 2p70-d 3s2x-1 1o7u-d 6swb-1 4inx-d 1ewx-d 3lua-d 4ym2-1 2h8v-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

2pl9C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (5) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Chemotaxis protein cheY

B: Chemotaxis protein cheY

C: Chemotaxis protein cheY

D: Chemotaxis protein cheY

E: Chemotaxis protein cheZ

F: Chemotaxis protein cheZ

hetero molecules

59.3 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Chemotaxis protein cheY

E: Chemotaxis protein cheZ

hetero molecules

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

2

B: Chemotaxis protein cheY

F: Chemotaxis protein cheZ

hetero molecules

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

3

C: Chemotaxis protein cheY

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

4

D: Chemotaxis protein cheY

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

Unit cell

Length a, b, c (Å)	34.760, 53.672, 65.641
Angle α, β, γ (deg.)	90.22, 102.92, 90.18
Int Tables number	1
Space group name H-M	P1

Details

The asymmetric unit contains four biological units, two of which are unbound CheY chains (chain C and chain D) and the other two are peptide-bound (chains A & E and chains B & F).

#1: Protein	Chemotaxis protein cheY Mass: 14009.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: cheY / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P0A2D5
#2: Protein/peptide	Chemotaxis protein cheZ Mass: 1622.687 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence corresponds to the C-terminal 15 residues of the CheZ protein occurring naturally in Salmonella enterica serovar Typhumurium. References: UniProt: P07800
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.01 Å³/Da / Density % sol: 38.9 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 37.5 % PEG 8000, 0.1 M ammonium thiocyanate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X4A / Wavelength: 0.97931 Å

Detector

Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2006

Radiation

Monochromator: KOHZU double crystal monochromator with a sagittally focused second crystal. Crystal type Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97931 Å / Relative weight: 1

Reflection

Resolution: 2.688→30 Å / Num. all: 12741 / Num. obs: 12578 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / R_merge(I) obs: 0.061 / Χ²: 1.058 / Net I/σ(I): 12.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.688-2.8	3.9	0.508	1259	1.075	1	98.4
2.8-2.91	3.9	0.393	1266	1.091	1	98.5
2.91-3.04	3.9	0.26	1238	1.095	1	98.3
3.04-3.2	3.9	0.206	1262	1.088	1	98.7
3.2-3.4	3.9	0.129	1257	1.091	1	98.8
3.4-3.66	3.9	0.082	1249	1.046	1	98.9
3.66-4.03	3.9	0.055	1261	1.092	1	99.1
4.03-4.61	3.9	0.04	1253	1.071	1	99.4
4.61-5.8	3.9	0.041	1296	0.992	1	99.5
5.8-30	3.8	0.035	1237	0.935	1	98.1

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Phasing

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.69 Å	28.59 Å
Translation	2.69 Å	28.59 Å

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 12578

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.79-100	62.7	0.685	508
6.21-7.79	76.3	0.553	512
5.44-6.21	78.8	0.643	508
4.94-5.44	66.2	0.658	505
4.6-4.94	61.2	0.684	513
4.32-4.6	61.5	0.658	511
4.11-4.32	59.5	0.652	505
3.93-4.11	59.9	0.653	515
3.78-3.93	64.4	0.601	502
3.65-3.78	71.5	0.559	511
3.53-3.65	66.4	0.584	503
3.43-3.53	71.3	0.608	517
3.34-3.43	66.5	0.58	513
3.26-3.34	64.8	0.6	528
3.18-3.26	67.4	0.56	544
3.11-3.18	67	0.54	552
3.04-3.11	70.5	0.519	562
2.97-3.04	71.7	0.548	590
2.91-2.97	69.3	0.554	558
2.86-2.91	68.6	0.533	620
2.8-2.86	74.2	0.467	634
2.75-2.8	72.4	0.512	619
2.69-2.75	78.1	0.449	748

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
DM	6	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
ADSC	Quantum	data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.688→28.59 Å / Cor.coef. F_o:F_c: 0.948 / Cor.coef. F_o:F_c free: 0.892 / SU B: 42.459 / SU ML: 0.411 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.285	1246	9.9 %	RANDOM
R_work	0.205	-	-	-
all	0.213	12578	-	-
obs	0.213	12578	98 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 33.641 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	-0.07 Å²	-0.03 Å²
2-	-	0.2 Å²	-0.03 Å²
3-	-	-	-0.23 Å²

Refinement step

Cycle: LAST / Resolution: 2.688→28.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4048	0	2	16	4066

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	4096
X-RAY DIFFRACTION	r_angle_refined_deg	1.033	1.988	5510
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.349	5	522
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.472	25.977	174
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.617	15	772
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.088	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	640
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3002
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1933
X-RAY DIFFRACTION	r_nbtor_refined	0.306	0.2	2798
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.142	0.2	162
X-RAY DIFFRACTION	r_metal_ion_refined	0.098	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.191	0.2	72
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.236	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	0.332	1.5	2702
X-RAY DIFFRACTION	r_mcangle_it	0.591	2	4160
X-RAY DIFFRACTION	r_scbond_it	1.029	3	1561
X-RAY DIFFRACTION	r_scangle_it	1.511	4.5	1350

LS refinement shell

Resolution: 2.688→2.758 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.368	75	-
R_work	0.327	714	-
obs	-	789	87.28 %

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	2.8699	2.8515	-4.6259	19.8875	0.8653	9.2792	0.0783	0.6431	-0.6486	-1.1143	-0.2501	1.5509	0.0387	-1.0233	0.1719	-0.31	0.0142	-0.1928	-0.1439	-0.0309	0.009	-6.819	15.799	-26.056
2	10.25	0.9984	-4.1412	20.6606	1.3	10.4739	1.5911	1.1152	0.7045	-3.7912	-0.8239	1.0023	-0.9919	-0.6618	-0.7672	0.3976	0.2648	-0.0588	-0.1158	0.0271	-0.0801	-3.861	27.306	-29.925
3	4.7578	2.1125	0.4964	24.2649	4.0849	7.2911	0.2706	-0.0776	0.5449	-0.597	0.0245	-0.3179	-0.8598	-0.1787	-0.2951	-0.2593	0.0213	0.0674	-0.1997	0.013	-0.2319	-1.958	28.438	-20.418
4	11.3309	-9.6336	-1.7395	21.8826	5.2086	1.7194	-0.2884	-0.7256	0.7552	2.4246	0.3682	-1.7439	0.8561	1.0376	-0.0798	0.0106	-0.0191	-0.1486	0.2731	0.0092	-0.1068	3.897	24.339	-9.93
5	16.8004	-6.6196	-3.9982	20.2184	9.7885	9.9655	0.1107	-0.3793	0.3159	2.3533	-0.0076	1.4536	0.8984	-0.989	-0.1031	-0.1512	-0.1218	0.0388	0.1415	0.2353	0.0058	-7.268	15.552	-13.637
6	8.3702	-0.293	-5.7764	18.63	-2.1616	11.5183	0.2776	-0.9066	-1.0096	0.9945	-0.3378	-1.2492	0.052	1.1305	0.0602	-0.3055	-0.009	-0.2251	-0.1939	0.0202	-0.0094	7.463	-10.985	-28.419
7	10.5952	-5.2435	0.0174	18.69	-5.1844	11.602	1.2461	-0.9336	1.2527	3.8962	-0.6391	-1.0348	-1.4581	0.8581	-0.607	0.3347	-0.2656	-0.092	-0.1001	-0.0735	-0.0512	4.5	0.428	-24.524
8	4.842	-0.8596	-1.2796	23.7069	-4.2224	5.9167	0.4724	0.1029	0.4774	0.8456	-0.1417	0.2843	-1.0163	0.0895	-0.3307	-0.3032	-0.0256	0.0767	-0.169	0.0059	-0.2274	2.567	1.632	-34.108
9	2.8175	1.1352	-2.064	10.2826	-4.0876	9.4065	-0.0882	1.3511	0.1092	-1.6813	0.887	1.3748	-0.2161	-1.3205	-0.7988	-0.0481	0.0697	-0.0958	0.1482	0.0359	0.0413	-2.841	-4.349	-43.336
10	12.2099	3.1975	-0.18	24.4227	-7.9426	5.4888	0.3186	0.8584	-0.0772	-1.6391	-0.395	-2.1926	0.3837	0.8178	0.0765	-0.2511	0.1508	0.0877	0.29	-0.2127	0.1193	9.686	-11.156	-41.238
11	9.0944	-8.0302	-7.5925	17.6874	-1.426	19.77	-0.2078	0.5452	-0.9349	-2.4177	-0.0384	1.2362	1.2139	-0.4698	0.2463	0.0968	-0.2489	-0.2498	0.2588	0.1396	0.1528	15.472	-2.268	-12.96
12	9.7596	-1.9093	-6.4614	18.219	4.9427	18.0125	-0.4607	1.2627	-0.5991	-3.3323	0.3606	1.6812	0.8616	-1.9753	0.1001	0.2536	-0.1332	-0.278	0.5616	0.1701	0.4046	11.428	-1.805	-13.633
13	14.195	-2.9811	0.2169	30.9475	-0.2631	39.7512	0.2002	0.0537	0.3035	1.9674	0.093	1.8279	0.0712	-1.5743	-0.2932	-0.3272	0.0436	0.096	0.2127	0.1877	0.0708	13.444	0.865	-5.32
14	9.0508	-4.9117	0.9181	11.1472	-0.9554	20.5228	-0.6413	-1.0596	-0.2355	2.2638	0.6316	1.17	-0.9035	-0.7042	0.0097	0.3823	0.1935	0.1883	0.4738	0.3181	0.3623	12.163	1.42	1.454
15	9.187	-0.9347	-8.263	10.2739	-9.4856	29.5841	0.1396	-0.1692	-2.1358	0.1472	-0.2468	0.7786	3.4784	-0.358	0.1072	1.0585	0.1087	0.1663	0.5782	0.11	0.6364	18.235	-11.503	-3.381
16	12.8116	3.9543	-5.4817	14.0727	6.5524	13.659	-0.4986	-0.8557	-1.1206	1.2894	0.4477	-0.941	1.6507	0.4038	0.0509	0.3891	0.2584	-0.0421	0.2464	-0.136	0.1639	19.942	24.726	-41.522
17	15.1784	4.9105	-4.6324	19.5453	-0.9487	19.0899	-0.7713	-1.2857	-0.9746	1.8793	0.5415	-2.0695	0.9067	1.2409	0.2299	0.3562	0.1764	-0.199	0.4423	-0.163	0.3439	23.976	25.235	-40.872
18	16.9095	11.04	-3.3319	8.0243	3.2929	37.283	1.3436	-1.0553	-0.041	-4.2567	0.2246	-2.2112	-0.2987	1.4775	-1.5683	-0.1623	-0.0157	-0.0461	0.1187	-0.2457	0.1583	21.978	27.859	-49.225
19	7.7938	2.1778	-3.0678	11.9847	0.1082	23.5286	-0.7024	0.7247	-0.0429	-2.2108	0.8616	-1.4141	-0.6979	0.657	-0.1592	0.2514	-0.1841	0.1394	0.4743	-0.3247	0.3309	23.735	28.769	-56.05
20	25.8829	-17.0278	-6.3043	23.3069	8.1789	32.3628	-0.4201	1.6318	-2.264	-0.3043	-0.4035	0.4646	3.9553	-0.249	0.8236	0.8508	-0.3941	0.1725	0.2815	-0.3288	0.5718	16.69	16.272	-51.238

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	2 - 31	1 - 30
2	2	A	A	32 - 47	31 - 46
3	3	A	A	48 - 87	47 - 86
4	4	A	A	88 - 105	87 - 104
5	5	A	A	106 - 129	105 - 128
6	6	B	B	2 - 31	1 - 30
7	7	B	B	32 - 47	31 - 46
8	8	B	B	48 - 87	47 - 86
9	9	B	B	88 - 109	87 - 108
10	10	B	B	110 - 129	109 - 128
11	11	C	C	2 - 20	1 - 19
12	12	C	C	21 - 50	20 - 49
13	13	C	C	51 - 60	50 - 59
14	14	C	C	61 - 108	60 - 107
15	15	C	C	109 - 129	108 - 128
16	16	D	D	2 - 20	1 - 19
17	17	D	D	21 - 50	20 - 49
18	18	D	D	51 - 60	50 - 59
19	19	D	D	61 - 106	60 - 105
20	20	D	D	107 - 129	106 - 128

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