PDB-3ehf: Crystal structure of DesKC in complex with AMP-PCP

ID or keywords:

Entry

Database: PDB / ID: 3ehf

Title

Crystal structure of DesKC in complex with AMP-PCP

Components

Sensor kinase (YocF protein)

Keywords

TRANSFERASE / four-helix bundle / GHL ATPase domain / Kinase

Function / homology

Function and homology information

histidine kinase / phosphorelay sensor kinase activity / phosphoprotein phosphatase activity / protein dimerization activity / protein kinase activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.1 Å

Authors

Albanesi, D. / Alzari, P.M. / Buschiazzo, A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural plasticity and catalysis regulation of a thermosensor histidine kinase
Authors: Albanesi, D. / Martin, M. / Trajtenberg, F. / Mansilla, M.C. / Haouz, A. / Alzari, P.M. / de Mendoza, D. / Buschiazzo, A.

History

Deposition	Sep 12, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 15, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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	3ehf.cif.gz	223 KB	Display	PDBx/mmCIF format
PDB format	pdb3ehf.ent.gz	176.7 KB	Display	PDB format
PDBx/mmJSON format	3ehf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ehf_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	3ehf_full_validation.pdf.gz	1.2 MB	Display
Data in XML	3ehf_validation.xml.gz	24.7 KB	Display
Data in CIF	3ehf_validation.cif.gz	31.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eh/3ehf ftp://data.pdbj.org/pub/pdb/validation_reports/eh/3ehf	HTTPS FTP

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Related structure data

Related structure data	3ehhC 3ehjC 3gieC 3gifC 3gigC 3ehg C: citing same article (ref.)
Similar structure data	5mto-d 5fn8-3 5fn8-4 3gl9-d 1npr-d 5me8-d 6yik-d 6gtd-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (1) #183 - Mar 2015 Phototropin similarity (1) #118 - Oct 2009 Sodium-Potassium Pump similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: Sensor kinase (YocF protein)

B: Sensor kinase (YocF protein)

C: Sensor kinase (YocF protein)

D: Sensor kinase (YocF protein)

hetero molecules

91.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Sensor kinase (YocF protein)

B: Sensor kinase (YocF protein)

hetero molecules

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

2

C: Sensor kinase (YocF protein)

D: Sensor kinase (YocF protein)

hetero molecules

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

Unit cell

Length a, b, c (Å)	75.800, 44.700, 131.450
Angle α, β, γ (deg.)	90.00, 103.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	C
2	2	D
1	3	A
2	3	D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	4	A	A	182 - 240	9 - 67
2	1	SER	SER	4	B	B	182 - 240	9 - 67
1	2	SER	SER	4	C	C	185 - 240	12 - 67
2	2	SER	SER	4	D	D	185 - 240	12 - 67
1	3	MG	MG	5	A	A - F	245 - 501	72
2	3	MG	MG	5	D	D - J	245 - 501	72

NCS ensembles :

ID
1
2
3

#1: Protein	Sensor kinase (YocF protein) / DesK histidine kinase Mass: 22585.189 Da / Num. of mol.: 4 / Fragment: entire cytoplasmic region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yocF / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O34757, histidine kinase
#2: Chemical	ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.92 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, MES, pH 6.5, vapor diffusion, hanging drop, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-4 / Wavelength: 0.9793 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2007 / Details: torodial focusing mirror

Radiation

Monochromator: channel-cut / Protocol: SAD / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 3.1→26.7 Å / Num. obs: 15927 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / B_iso Wilson estimate: 54.042 Å² / R_merge(I) obs: 0.11

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
3.1-3.2		0.444	7.1	19418	1439	99.4
3.2-3.3		0.399	8.3	16918	1246	99
3.3-3.4		0.298	11.5	15574	1125	99.6
3.4-3.5		0.242	14.4	13895	982	99.1
3.5-4		0.175	19.5	52779	3651	99.5
4-6		0.091	29.7	75236	5196	99.2
6-10		0.059	37.2	24667	1770	98.7
10-20		0.046	44.2	5825	451	98.3
	20	0.058	25.8	339	67	90.5

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Phasing

Phasing

Method:

SAD

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	3.5	43.73	9775	1116
ANO_1	0.814	0	3.5	43.73	9769	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	Reflection acentric	Reflection centric
ISO_1	14.78-43.73	0	98	58
ISO_1	10.76-14.78	0	188	59
ISO_1	8.88-10.76	0	232	53
ISO_1	7.73-8.88	0	302	54
ISO_1	6.93-7.73	0	337	56
ISO_1	6.34-6.93	0	373	58
ISO_1	5.88-6.34	0	414	60
ISO_1	5.51-5.88	0	442	53
ISO_1	5.2-5.51	0	499	59
ISO_1	4.93-5.2	0	472	59
ISO_1	4.71-4.93	0	553	50
ISO_1	4.51-4.71	0	539	57
ISO_1	4.33-4.51	0	591	56
ISO_1	4.18-4.33	0	590	49
ISO_1	4.04-4.18	0	626	46
ISO_1	3.91-4.04	0	683	63
ISO_1	3.79-3.91	0	664	49
ISO_1	3.69-3.79	0	697	58
ISO_1	3.59-3.69	0	740	62
ISO_1	3.5-3.59	0	735	57
ANO_1	14.78-43.73	0.392	98	0
ANO_1	10.76-14.78	0.595	188	0
ANO_1	8.88-10.76	0.549	232	0
ANO_1	7.73-8.88	0.62	301	0
ANO_1	6.93-7.73	0.618	337	0
ANO_1	6.34-6.93	0.669	373	0
ANO_1	5.88-6.34	0.737	413	0
ANO_1	5.51-5.88	0.725	442	0
ANO_1	5.2-5.51	0.814	499	0
ANO_1	4.93-5.2	0.816	471	0
ANO_1	4.71-4.93	0.827	551	0
ANO_1	4.51-4.71	0.875	539	0
ANO_1	4.33-4.51	0.853	591	0
ANO_1	4.18-4.33	0.899	590	0
ANO_1	4.04-4.18	0.961	625	0
ANO_1	3.91-4.04	0.955	683	0
ANO_1	3.79-3.91	0.974	664	0
ANO_1	3.69-3.79	0.997	697	0
ANO_1	3.59-3.69	0.976	740	0
ANO_1	3.5-3.59	0.984	735	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	51.262	26.368	15.051	SE	154.98	2.39
2	17.852	24.905	-5.685	SE	138.85	1.46
3	39.187	21.823	12.289	SE	42.23	0.46
4	36.519	24.336	15.306	SE	147.87	0.25
5	29.989	17.487	11.964	SE	155.32	2.05
6	28.352	22.389	12.548	SE	131.66	1.83
7	53.092	23.853	19.406	SE	137.45	1.64
8	58.462	30.44	27.688	SE	53.85	0.43
9	59.896	38.656	31.208	SE	67.91	0.76
10	34.472	35.937	78.383	SE	159.42	1.48
11	38.561	33.433	79.844	SE	145.48	1.47
12	49.907	49.421	111.014	SE	103.73	2.05
13	37.43	41.296	90.183	SE	39.08	0.63
14	32.453	47.931	97.071	SE	114.79	1.67
15	33.392	43.34	100.151	SE	126.15	1.87

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 23982

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
10.13-100	47.7	0.74	505
7.96-10.13	40.7	0.87	503
6.9-7.96	42.4	0.884	512
6.24-6.9	39.4	0.878	513
5.74-6.24	38.1	0.894	579
5.34-5.74	34.2	0.903	606
5.02-5.34	34.4	0.895	640
4.75-5.02	27	0.907	686
4.52-4.75	27.3	0.908	693
4.32-4.52	25.5	0.911	776
4.14-4.32	28.6	0.914	768
3.98-4.14	26.3	0.92	804
3.84-3.98	24.6	0.932	863
3.72-3.84	24.3	0.931	874
3.6-3.72	24.9	0.92	901
3.5-3.6	23.3	0.92	923
3.4-3.5	25.9	0.912	932
3.31-3.4	25.4	0.914	1000
3.23-3.31	27.5	0.903	998
3.16-3.23	29	0.903	1010
3.09-3.16	28.2	0.903	1078
3.02-3.09	30.3	0.897	1058
2.96-3.02	29.6	0.891	1085
2.9-2.96	31	0.882	1130
2.84-2.9	34.5	0.87	1124
2.79-2.84	37.8	0.852	1162
2.7-2.79	44	0.807	2259

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
SHARP		phasing
DM	6	phasing
REFMAC	5.5.0053	refinement
PDB_EXTRACT	3.006	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 3.1→15 Å / Cor.coef. F_o:F_c: 0.901 / Cor.coef. F_o:F_c free: 0.874 / Occupancy max: 1 / Occupancy min: 0.29 / SU B: 43.355 / SU ML: 0.379 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Hydrogens have been added in the riding positions atom record contains sum of TLS and residual B anisou record contains sum of TLS and residual U

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.297	816	5.2 %	RANDOM
R_work	0.242	14957	-	-
obs	0.245	15773	99.24 %	-

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 max: 129.07 Å² / B_iso mean: 59.423 Å² / B_iso min: 10.36 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.24 Å²	0 Å²	3.65 Å²
2-	-	-0.13 Å²	0 Å²
3-	-	-	4.01 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3950	0	77	3	4030

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.024	0.024	4444
X-RAY DIFFRACTION	r_angle_refined_deg	1.654	2.003	5470
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.058	5	511
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.231	25.19	158
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.443	15	775
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.701	15	26
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	665
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2832
X-RAY DIFFRACTION	r_mcbond_it	0.851	1.5	2953
X-RAY DIFFRACTION	r_mcangle_it	0.984	2	4106
X-RAY DIFFRACTION	r_scbond_it	1.677	3	1491
X-RAY DIFFRACTION	r_scangle_it	2.771	4.5	1363

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	456	MEDIUM POSITIONAL	0.42	0.5
1	A	456	MEDIUM THERMAL	0.77	2
2	C	406	MEDIUM POSITIONAL	0.39	0.5
2	C	406	MEDIUM THERMAL	0.8	2
3	A	431	MEDIUM POSITIONAL	0.36	0.5
3	A	431	LOOSE POSITIONAL	0.64	5
3	A	431	MEDIUM THERMAL	1.16	2
3	A	431	LOOSE THERMAL	1.8	10

LS refinement shell

Resolution: 3.1→3.177 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.345	52	-
R_work	0.265	1077	-
all	-	1129	-
obs	-	-	99.3 %

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	12.2049	-2.2942	-4.4228	3.5823	0.3073	6.451	-0.0931	-0.5362	-0.3295	0.0093	0.0164	0.4955	0.259	-0.5222	0.0767	0.0996	-0.0349	-0.08	0.1379	0.0027	0.1465	68.572	25.615	4.791
2	7.8967	0.0512	-4.0917	5.182	-0.9562	5.4326	0.3686	-0.1798	-0.0105	-0.2154	-0.4488	0.0085	-0.1215	-0.7918	0.0802	0.664	0.016	0.0573	0.3397	-0.0101	0.1481	55.33	34.869	67.565
3	5.8629	0.8103	2.5149	3.7657	2.0975	10.3718	0.3712	0.2193	0.4244	0.1364	-0.2416	-0.0775	0.3707	1.1153	-0.1296	0.3368	0.1445	-0.0115	0.7901	0.0426	0.4009	27.516	22.868	9.23
4	9.2618	3.6422	-0.0756	5.2057	0.8959	5.8576	-0.0693	0.7978	0.0569	-0.3022	0.0333	0.1374	0.3532	-0.0683	0.0359	0.4029	0.0948	-0.0626	0.7513	-0.0394	0.306	36.235	45.082	101.022
5	17.5009	2.3329	3.0958	4.5643	2.0312	7.9164	0.1	0.4866	-0.4176	-0.8476	-0.1531	0.6086	0.2891	-0.7214	0.0531	0.9421	0.0543	0.1223	1.0061	-0.0526	0.6288	64.918	32.717	37.588

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	182 - 242
2	X-RAY DIFFRACTION	1	B	182 - 242
3	X-RAY DIFFRACTION	2	C	185 - 241
4	X-RAY DIFFRACTION	2	D	185 - 241
5	X-RAY DIFFRACTION	3	A	245 - 501
6	X-RAY DIFFRACTION	4	D	245 - 501
7	X-RAY DIFFRACTION	5	B	251 - 501

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