PDB-2r8r: Crystal structure of the N-terminal region (19..243) of sensor pr...

ID or keywords:

Entry

Database: PDB / ID: 2r8r

Title

Crystal structure of the N-terminal region (19..243) of sensor protein KdpD from Pseudomonas syringae pv. tomato str. DC3000

Components

Sensor protein

Keywords

TRANSFERASE / KdpD /

sensor protein / pfam02702 / MCSG /

Structural Genomics / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics /

Kinase /

Phosphorylation

Function / homology

Function and homology information

histidine kinase / phosphorelay sensor kinase activity / membrane => GO:0016020
Similarity search - Function

Biological species

Pseudomonas syringae pv. tomato (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Nocek, B. / Mulligan, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of the N-terminal region (19..243) of sensor protein KdpD from Pseudomonas syringae pv. tomato str. DC3000.
Authors: Nocek, B. / Mulligan, R. / Moy, S. / Joachimiak, A.

History

Deposition	Sep 11, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 25, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2r8r.cif.gz	104.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2r8r.ent.gz	87.2 KB	Display	PDB format
PDBx/mmJSON format	2r8r.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r8/2r8r ftp://data.pdbj.org/pub/pdb/validation_reports/r8/2r8r	HTTPS FTP

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Related structure data

Similar structure data	3zpy-1 6rvg-d 4e9o-d 2d3k-d 3owv-2 3wq7-1 3wt3-2 5dxd-2 3eis-3 6eo8-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC86836.1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (8) #183 - Mar 2015 Phototropin similarity (11) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (3)

Deposited unit

A: Sensor protein

B: Sensor protein

hetero molecules

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

1

A: Sensor protein

hetero molecules

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

2

B: Sensor protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.859, 56.859, 372.783
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-918- HOH
2	1	A-920- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLY / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 2 - 105 / Label seq-ID: 5 - 108

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

Details

Authors state that biological unit of this polypeptide is unknown.

#1: Protein	Sensor protein / Mass: 25377.895 Da / Num. of mol.: 2 / Fragment: N-terminal region: Residues 19-243 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: kdpD, PSPTO_2245 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q883V3, histidine kinase
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.97 Å³/Da / Density % sol: 58.56 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1M Ammonium sulfate, 0.5% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97940, 0.97950

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2007 / Details: mirrors

Radiation

Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9794	1
2	0.9795	1

Reflection

Resolution: 2.3→30 Å / Num. all: 28395 / Num. obs: 28395 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / B_iso Wilson estimate: 39.8 Å² / R_merge(I) obs: 0.089 / Net I/σ(I): 24.3

Reflection shell

Resolution: 2.3→2.34 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.234 / Mean I/σ(I) obs: 5.24 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL2Map		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.3→30 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.931 / SU B: 9.045 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.221 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21642	1440	5.1 %	RANDOM
R_work	0.17073	-	-	-
all	0.17303	26955	-	-
obs	0.17303	26955	99.01 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 17.391 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.13 Å²	0 Å²	0 Å²
2-	-	0.13 Å²	0 Å²
3-	-	-	-0.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3222	0	41	436	3699

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	3303
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2193
X-RAY DIFFRACTION	r_angle_refined_deg	1.53	1.98	4484
X-RAY DIFFRACTION	r_angle_other_deg	0.989	3	5346
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.865	5	413
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.131	23.987	153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.433	15	562
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.491	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	525
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3651
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	632
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	633
X-RAY DIFFRACTION	r_nbd_other	0.197	0.2	2339
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	1533
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	1786
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	302
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.082	0.2	2
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.359	0.2	51
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.222	0.2	17
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.047	1.5	2275
X-RAY DIFFRACTION	r_mcbond_other	0.195	1.5	841
X-RAY DIFFRACTION	r_mcangle_it	1.327	2	3310
X-RAY DIFFRACTION	r_scbond_it	2.272	3	1316
X-RAY DIFFRACTION	r_scangle_it	3.252	4.5	1174
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 98 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
medium positional	2.9	0.5
medium thermal	1.07	2

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.273	113	-
R_work	0.185	1886	-
obs	-	-	97.18 %

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	0.7933	-0.093	0.3943	1.4867	0.536	0.8871	-0.0537	0.0464	0.0858	-0.0215	0.0497	0.1316	0.002	-0.0567	0.004	0.0141	0.0096	0.0217	0.0674	0.0104	0.0491	-3.8214	8.6822	168.3305
2	3.4755	0.3107	3.7895	1.1605	-0.1742	7.9964	0.1066	0.2904	-0.0398	-0.1379	0.0988	0.0176	0.0044	0.5099	-0.2054	0.0549	-0.0092	0.0306	0.0593	-0.0028	0.0272	4.9287	11.9289	159.8789
3	5.0285	-0.9334	4.3266	2.1513	1.301	5.9608	-0.3149	0.4129	0.4415	0.0408	0.1797	-0.1888	-0.5501	0.351	0.1352	0.0381	-0.051	0.0306	0.0469	0.0026	0.0606	6.0227	18.6223	167.9342
4	23.1183	-9.3061	-4.8766	8.7114	2.3967	2.3155	-0.2623	0.8109	0.9343	-0.2999	0.0106	-0.3683	0.1984	0.2455	0.2517	-0.104	0.0004	-0.026	0.1966	-0.0418	0.0366	21.5147	11.2213	170.0034
5	1.1152	-0.7969	0.4507	1.2835	-0.2118	2.0367	-0.1194	0.1425	0.1035	0.0619	0.1263	0.0059	-0.1107	0.2598	-0.0069	-0.0114	0.0014	0.0221	0.089	-0.0438	0.0396	8.7168	10.8164	176.796
6	0.1213	-0.4418	-0.2857	1.8001	1.7562	3.3553	-0.0679	0.0762	-0.0134	0.2571	0.0458	0.0511	-0.0046	0.309	0.0221	0.0284	0.0235	0.0158	0.095	-0.0306	0.0265	8.4179	4.7334	179.6152
7	0.5086	0.1178	0.6868	1.182	-0.0868	0.9796	0.0501	0.0219	-0.0382	-0.1088	0.0571	0.0585	-0.0988	0.0913	-0.1072	0.0088	0.0269	0.0332	0.091	-0.0328	0.0334	1.9647	3.4946	173.404
8	3.8166	0.8463	-4.1059	6.9337	3.4802	9.7726	-0.1529	-0.4469	-0.5011	0.176	0.2737	-0.2315	0.1722	0.6738	-0.1208	0.0104	0.1366	-0.037	0.0801	-0.0327	0.028	11.727	-13.333	167.2901
9	0.2619	0.0652	-1.0239	2.8821	-0.1347	4.0084	-0.0583	-0.1254	-0.316	0.4557	0.2085	0.0504	0.2331	0.3164	-0.1502	0.0385	0.1009	0.0014	0.1271	-0.0149	-0.0107	8.6191	-5.4266	174.8494
10	0.9165	0.1339	-0.7014	0.8361	1.9268	5.5799	-0.0879	0.0125	-0.0567	0.0908	-0.0841	0.1236	0.1754	0.0087	0.172	0.0172	0.0277	0.0078	0.0566	0.0099	0.0627	-3.9388	-3.1059	167.7159
11	6.4105	0.0403	-3.6767	7.1901	-4.2447	4.5876	0.195	0.5809	-0.0249	-0.0122	0.0243	0.3382	-0.1265	-0.156	-0.2192	-0.0433	0.0439	-0.0274	0.222	-0.0667	0.0306	4.7181	-1.5855	148.4719
12	38.1324	-10.4952	11.3516	5.0602	2.9104	20.1493	-0.6854	-1.0031	2.3799	0.528	0.1961	-0.9059	0.615	-0.2674	0.4893	-0.0782	-0.0127	0.0129	-0.0455	-0.0807	0.1453	15.4375	0.5617	156.8119
13	18.7377	0.2314	2.4113	5.5757	4.6699	4.1739	-0.0318	0.2897	-0.0856	0.1305	0.0202	0.1765	0.2734	0.4238	0.0116	0.0123	0.0614	0.0015	0.1306	-0.0733	-0.0074	14.2394	-7.2659	155.0797
14	10.7836	-0.3332	-2.432	1.3607	-0.6925	1.9546	-0.0882	0.258	-0.3135	0.1529	-0.0422	-0.2431	0.4502	-0.0398	0.1304	0.0112	0.0815	-0.0107	0.0579	-0.0998	0.0916	4.4301	-12.2615	156.1691
15	5.8804	0.9651	-5.5659	6.0219	-3.9569	7.3312	0.2025	-0.491	-0.9945	0.0938	0.241	0.5579	0.2405	0.0711	-0.4435	0.0246	0.0222	-0.0215	0.0267	0.0619	0.1001	-3.0741	-11.4114	167.6301
16	6.1732	-1.3269	0.9417	4.4581	7.0298	14.9715	-0.0069	0.2307	-0.024	-0.1119	0.2505	-0.4598	-0.0873	0.873	-0.2436	0.04	-0.0172	0.0497	-0.0066	0.0162	0.0505	-9.5119	-8.3131	139.5088
17	0.8305	0.9157	-1.1389	1.4411	-1.93	3.4144	0.0001	-0.0432	0.0383	0.0047	0.0141	0.0199	-0.0754	0.058	-0.0143	0.0269	-0.0053	0.0094	0.0491	-0.0076	0.0584	-10.6984	3.5502	149.7125
18	0.8964	0.9847	1.3457	3.5123	1.5108	2.0208	-0.0195	-0.0253	0.0866	0.1429	-0.1031	0.1678	-0.1475	-0.2656	0.1226	0.0331	0.0192	0.0264	0.0426	-0.012	0.0695	-19.3906	9.7207	148.3922
19	13.8316	7.1648	-12.2746	5.7445	-5.6516	19.216	-0.3192	-0.7122	0.5648	0.1666	-0.4111	-0.1768	-0.1899	-0.0495	0.7303	-0.1262	0.041	-0.0173	0.148	-0.0182	0.1891	-39.4308	2.8974	146.0015
20	8.2545	0.3613	-8.6149	1.0059	1.3017	11.8372	0.0181	0.0633	0.076	-0.2847	-0.1021	0.2944	0.1954	-0.2175	0.084	-0.0307	0.0232	-0.0429	0.0531	-0.0114	0.1194	-28.2654	2.2127	140.634
21	1.7825	0.9562	-0.0648	0.6726	-0.1403	2.6294	-0.0602	-0.057	0.0947	-0.101	-0.033	0.113	-0.0119	-0.0006	0.0932	0.0178	0.0172	0.012	0.0068	-0.003	0.0739	-19.9361	-0.8216	141.8611
22	1.1054	0.0757	1.9041	3.0517	-0.1557	3.3067	-0.0128	0.1336	-0.1222	-0.1022	-0.014	-0.0662	0.236	-0.4026	0.0268	0.0121	-0.0282	0.0115	0.0938	-0.0348	0.045	-28.4023	-7.4595	141.9319
23	0.3642	0.1641	0.5195	0.3711	0.3996	1.5253	-0.0231	-0.018	-0.0056	-0.0489	-0.0197	0.0332	0.0453	-0.0137	0.0428	0.0377	-0.0076	0.0322	0.0519	-0.0012	0.0435	-17.4445	-6.0048	145.1498
24	3.5969	-2.7159	-4.0425	3.9319	4.1144	13.0783	0.0047	-0.0978	-0.3795	0.062	-0.2335	0.1121	0.3829	-0.5182	0.2287	0.0309	-0.0698	0.0614	0.0478	-0.0092	0.0498	-26.2648	-14.8126	162.795
25	5.9205	0.4396	-2.109	0.1393	0.3751	3.4032	0.1232	0.1053	0.0286	0.0304	-0.1155	-0.035	0.0816	0.0108	-0.0076	0.0421	-0.0009	0.0394	0.019	0.0104	0.0832	-18.5221	-13.1109	150.0389
26	2.8974	-1.1094	-1.9407	1.1268	0.8946	1.4159	0.118	-0.2685	0.0793	0.141	-0.1482	-0.2161	-0.0136	-0.0476	0.0302	0.0229	-0.0301	0.0274	0.1155	-0.0315	0.0362	-15.9106	2.5133	167.1826
27	10.0665	4.9856	3.1353	2.4692	1.5528	0.9765	0.1699	0.6791	0.6565	-0.0145	-0.4082	0.8914	0.8204	0.1752	0.2383	0.0623	0.0113	0.0785	0.1907	-0.013	0.1179	-28.0766	0.1764	166.1623
28	9.8459	-4.4766	-4.6499	6.4929	6.6858	6.8847	-0.0656	-0.596	-0.365	0.162	-0.1458	-0.0235	0.2343	0.1973	0.2115	0.0276	-0.0562	0.0451	0.1377	0.0619	-0.0079	-19.9192	-7.0522	171.38
29	9.9205	-0.2005	-7.6609	21.5206	3.699	6.4998	0.2326	-0.9151	-0.8493	0.8964	-0.316	-0.7533	0.5534	0.2171	0.0834	0.0261	-0.0409	-0.0808	0.1231	0.1637	0.0812	-13.1231	-11.5275	165.282
30	0.9209	-3.6317	-4.5893	14.3213	18.0975	22.8694	-0.1914	-0.2982	0.1244	0.0224	0.9901	-1.1313	0.7807	-0.0895	-0.7987	0.0904	0.007	0.1023	-0.0137	0.0177	0.2758	-8.6547	-16.2095	155.9253

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	0 - 35	3 - 38
2	X-RAY DIFFRACTION	2	A	A	36 - 50	39 - 53
3	X-RAY DIFFRACTION	3	A	A	51 - 60	54 - 63
4	X-RAY DIFFRACTION	4	A	A	61 - 72	64 - 75
5	X-RAY DIFFRACTION	5	A	A	73 - 100	76 - 103
6	X-RAY DIFFRACTION	6	A	A	101 - 110	104 - 113
7	X-RAY DIFFRACTION	7	A	A	111 - 125	114 - 128
8	X-RAY DIFFRACTION	8	A	A	126 - 140	129 - 143
9	X-RAY DIFFRACTION	9	A	A	141 - 150	144 - 153
10	X-RAY DIFFRACTION	10	A	A	151 - 163	154 - 166
11	X-RAY DIFFRACTION	11	A	A	164 - 174	167 - 177
12	X-RAY DIFFRACTION	12	A	A	175 - 182	178 - 185
13	X-RAY DIFFRACTION	13	A	A	183 - 189	186 - 192
14	X-RAY DIFFRACTION	14	A	A	190 - 198	193 - 201
15	X-RAY DIFFRACTION	15	A	A	199 - 208	202 - 211
16	X-RAY DIFFRACTION	16	B	B	-1 - 5	2 - 8
17	X-RAY DIFFRACTION	17	B	B	6 - 35	9 - 38
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