PDB-4l85: Crystal structure of receiver domain of KdpE D52A mutant from E. coli

ID or keywords:

Entry

Database: PDB / ID: 4l85

Title

Crystal structure of receiver domain of KdpE D52A mutant from E. coli

Components

KDP operon transcriptional regulatory protein KdpE

Keywords

TRANSCRIPTION / Receiver domain

Function / homology

Function and homology information

phosphorelay response regulator activity / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / protein homodimerization activity / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.202 Å

Authors

Kumar, S. / Yernool, D.A.

Citation

Journal: Nat Commun / Year: 2014
Title: An asymmetric heterodomain interface stabilizes a response regulator-DNA complex.
Authors: Narayanan, A. / Kumar, S. / Evrard, A.N. / Paul, L.N. / Yernool, D.A.

History

Deposition	Jun 15, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 19, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 19, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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	4l85.cif.gz	157.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4l85.ent.gz	127.1 KB	Display	PDB format
PDBx/mmJSON format	4l85.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4l85_validation.pdf.gz	458.7 KB	Display	wwPDB validaton report
Full document	4l85_full_validation.pdf.gz	466.9 KB	Display
Data in XML	4l85_validation.xml.gz	17.9 KB	Display
Data in CIF	4l85_validation.cif.gz	24.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l8/4l85 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/4l85	HTTPS FTP

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Related structure data

Related structure data	4kfcC 4knyC C: citing same article (ref.)
Similar structure data	1ba2-2 7jz5-d 6swb-d 2b7l-1 1urp-3 5cv5-d 3pjy-d 4fna-3 6c7z-d 3n7h-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (10) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: KDP operon transcriptional regulatory protein KdpE

B: KDP operon transcriptional regulatory protein KdpE

C: KDP operon transcriptional regulatory protein KdpE

hetero molecules

44.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: KDP operon transcriptional regulatory protein KdpE

B: KDP operon transcriptional regulatory protein KdpE

hetero molecules

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

2

C: KDP operon transcriptional regulatory protein KdpE

hetero molecules

C: KDP operon transcriptional regulatory protein KdpE

hetero molecules

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

Unit cell

Length a, b, c (Å)	108.918, 108.918, 74.408
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	KDP operon transcriptional regulatory protein KdpE Mass: 13485.414 Da / Num. of mol.: 3 / Fragment: Response regulatory domain residues 3-121 / Mutation: D52A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0694, JW5096, kdpE / Production host: Escherichia coli (E. coli) / References: UniProt: P21866
#2: Chemical	... ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: I
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.15 Å³/Da / Density % sol: 60.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 15% PEG 8K, 0.1M NaCl, 0.1M TRIS pH 7.2-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 7.2 to 8.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.54984 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 18, 2012
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54984 Å / Relative weight: 1
Reflection	Resolution: 2.2→29.21 Å / Num. all: 26072 / Num. obs: 26052 / % possible obs: 99.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.8 % / B_iso Wilson estimate: 43.89 Å²
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 21.5 % / Mean I/σ(I) obs: 6.08 / Num. unique all: 2518 / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHENIX		model building
PHENIX	(phenix.refine: dev_1352)	refinement
HKL-2000		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.202→29.21 Å / SU ML: 0.22 / σ(F): 1.38 / Phase error: 22.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2191	2547	5.11 %	RANDOM
R_work	0.1736	-	-	-
obs	0.176	26052	99.72 %	-
all	-	26072	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.202→29.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2707	0	35	163	2905

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2734
X-RAY DIFFRACTION	f_angle_d	1.102	3683
X-RAY DIFFRACTION	f_dihedral_angle_d	14.549	1041
X-RAY DIFFRACTION	f_chiral_restr	0.073	429
X-RAY DIFFRACTION	f_plane_restr	0.005	484

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 (%)
2.2018-2.2441	0.2492	140	0.212	2504	X-RAY DIFFRACTION	95
2.2441-2.2899	0.2795	113	0.1949	2629	X-RAY DIFFRACTION	100
2.2899-2.3397	0.2045	106	0.1919	2687	X-RAY DIFFRACTION	100
2.3397-2.3941	0.2634	131	0.1986	2708	X-RAY DIFFRACTION	100
2.3941-2.4539	0.2726	126	0.1925	2619	X-RAY DIFFRACTION	100
2.4539-2.5202	0.2345	174	0.1959	2566	X-RAY DIFFRACTION	100
2.5202-2.5943	0.2542	153	0.1898	2674	X-RAY DIFFRACTION	100
2.5943-2.678	0.2494	151	0.1953	2624	X-RAY DIFFRACTION	100
2.678-2.7737	0.2492	139	0.2035	2621	X-RAY DIFFRACTION	100
2.7737-2.8846	0.2653	169	0.2041	2599	X-RAY DIFFRACTION	100
2.8846-3.0158	0.2568	161	0.1975	2630	X-RAY DIFFRACTION	100
3.0158-3.1746	0.2636	128	0.1821	2629	X-RAY DIFFRACTION	100
3.1746-3.3732	0.208	154	0.1781	2638	X-RAY DIFFRACTION	100
3.3732-3.6332	0.2203	151	0.1636	2636	X-RAY DIFFRACTION	100
3.6332-3.998	0.1956	141	0.1546	2651	X-RAY DIFFRACTION	100
3.998-4.5746	0.1586	133	0.1415	2621	X-RAY DIFFRACTION	100
4.5746-5.7563	0.2184	138	0.1553	2663	X-RAY DIFFRACTION	100
5.7563-29.2123	0.2114	139	0.1848	2618	X-RAY DIFFRACTION	100

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	4.8622	-5.4234	-5.9941	9.641	1.9976	2.0119	-0.0771	-0.4485	1.2862	-2.2006	0.7627	-0.293	-2.2806	-0.0221	-0.2876	0.6108	0.1711	-0.0676	0.8055	-0.1226	0.633	13.2513	103.4472	-0.4405
2	3.8419	1.2208	-4.0199	6.3623	0.9614	6.1904	0.6629	0.721	1.6179	-0.3155	-0.1832	0.3565	-1.371	-1.466	-0.4447	0.6084	0.1711	-0.1803	0.8821	0.0473	1.0189	14.656	111.2354	-1.8772
3	4.1365	-1.2519	-4.4888	6.0373	3.4285	5.9039	-0.6924	-0.6963	-0.0055	-0.3384	0.5206	0.3441	-0.2237	-0.0081	0.2704	0.3913	0.1564	-0.1322	0.9567	-0.0024	0.6557	11.4372	103.9948	-2.0172
4	2.909	1.1785	4.7919	4.3555	1.5114	7.8895	-0.4567	-0.5562	-0.1341	0.4553	0.7595	1.4827	0.5088	-1.5774	-0.1019	0.3769	0.182	0.0629	1.4296	0.1309	0.8436	4.4825	98.3164	6.0892
5	5.3282	-2.9941	-2.7668	9.0916	-1.1002	7.9167	-0.4792	-0.2224	-0.2293	0.0492	0.9596	0.3999	-0.2438	0.101	-0.2746	0.2447	0.1109	-0.0784	0.6341	0.0233	0.4685	13.3095	99.0302	4.3019
6	6.3902	2.0683	3.2994	6.2915	1.5949	3.8728	0.3259	-2.4634	-0.7567	1.9652	0.4057	0.8043	0.9666	-2.298	0.5285	0.0522	0.2233	0.1011	1.3101	0.2596	0.5642	13.8535	94.6393	11.2854
7	9.9209	-1.6269	2.7663	7.7779	-8.1563	8.7212	-1.084	-1.7236	2.2183	2.6397	0.7977	-0.0173	-1.5475	-0.6965	-0.4224	0.7608	0.5087	0.0704	1.3936	-0.1907	0.5261	23.4478	101.0495	18.9174
8	4.102	1.144	1.3473	8.8432	-4.1939	6.1214	-0.659	-0.5844	0.4179	0.4192	0.5547	0.0134	-0.5595	-0.2105	0.1768	0.4063	0.1484	-0.0661	0.8072	-0.1206	0.4904	24.1659	104.158	10.1149
9	3.9118	1.2697	0.4678	2.2843	1.9412	3.374	0.0358	0.6637	-0.2942	-0.5079	0.4438	0.3502	-0.1899	-0.2499	-0.4439	0.4087	0.1161	-0.0865	0.5941	-0.0171	0.4935	25.7341	98.5136	-0.3119
10	9.2219	0.2874	-0.8783	8.2562	-2.9132	6.7687	-0.7652	0.4199	-0.7623	-0.9486	-0.2596	-0.8273	-0.0576	0.139	0.4044	0.8084	0.4837	0.0095	0.8124	-0.3135	0.7396	32.3162	126.8825	-4.5074
11	9.9593	4.062	-0.9435	4.4162	-3.9368	7.802	-0.4257	1.3069	0.8731	-1.966	-0.2931	0.283	-0.5392	-0.2342	0.1084	1.3916	0.6005	-0.1994	0.8503	-0.2497	0.8593	27.5042	136.1915	-7.7511
12	6.229	4.5432	-4.0758	4.0298	-3.967	5.6669	-0.384	1.0493	-0.0447	-1.9311	0.4246	-0.1473	0.511	-0.4801	-0.0921	0.9449	0.2993	-0.1835	0.9388	-0.226	0.9775	25.3826	123.829	-5.5075
13	7.317	2.003	-0.2684	6.8584	-3.8944	8.2787	-0.665	-0.3476	-0.0027	0.9396	0.7555	0.3037	-0.1662	-0.7628	-0.1415	0.7578	0.2548	-0.1075	0.6658	-0.0454	0.7142	23.6237	128.8281	1.9612
14	0.4087	1.341	1.0953	5.8944	1.15	4.7401	0.0975	0.1847	-0.0131	0.4425	0.0231	1.6302	0.1712	-0.8304	-0.0881	0.5991	0.1938	-0.0805	0.6687	-0.133	1.0295	21.8657	123.3394	6.5796
15	2.3943	-3.927	-2.2863	8.7714	-0.0992	8.93	-0.3637	0.1369	1.7369	0.9164	0.0858	1.6467	-0.8292	-1.5534	-0.255	0.6269	0.314	-0.0865	0.832	-0.1067	1.0932	19.0556	134.7779	13.6257
16	3.8383	1.8707	-4.0582	3.4821	-0.201	9.4433	-0.0988	0.2243	-0.1592	0.0482	0.3063	-0.2991	-0.1686	-0.0376	-0.1195	0.6703	0.2322	-0.1366	0.5072	-0.1225	0.6927	31.9265	134.7897	6.4752
17	5.2836	-1.1014	-0.6935	5.1126	3.7457	8.1119	0.205	-0.9537	-0.5202	0.9043	-0.2056	0.0218	0.6278	0.1421	0.0151	0.4163	0.0265	-0.011	0.4551	0.0774	0.2874	43.2681	87.8938	16.8977
18	9.3597	-2.7783	-3.6468	3.6349	1.9456	8.6835	-0.1384	-0.3235	-0.3839	0.0269	-0.0481	0.2269	0.2997	-0.047	0.2159	0.259	0.0054	-0.0061	0.3513	-0.0002	0.2386	43.9509	85.3404	6.3039
19	5.6353	1.0735	-2.6083	3.0943	3.0848	5.648	1.2127	-0.1775	0.9614	-1.1096	0.2236	-2.3092	-4.7275	0.6288	1.0481	1.7242	-0.6983	-0.4386	0.6803	1.0618	1.8507	47.9141	102.6706	3.5018
20	6.6131	-0.7593	1.7945	3.113	1.5289	4.7598	0.3112	0.8233	-0.1284	-0.584	-0.2502	-0.2273	-0.0665	0.1823	-0.0301	0.2889	0.06	-0.0086	0.4288	-0.0147	0.2276	40.0403	90.8281	0.1216
21	3.213	-2.6381	1.4058	3.5109	-0.0594	3.4927	-0.3811	0.609	1.3841	0.062	0.2032	-1.5126	-1.3926	0.9	0.0551	0.5773	0.0274	-0.0989	0.6079	0.0571	0.6877	36.8875	103.9525	1.9329
22	4.5918	-3.542	-1.9333	7.3431	-3.515	6.3179	-0.3934	-0.6791	-0.0244	1.072	0.7062	0.1839	-0.6313	-0.6559	-0.2957	0.3512	0.1564	-0.0075	0.625	-0.0041	0.3575	32.2843	94.6878	12.6995

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 10 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 11 through 23 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 24 through 33 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 34 through 43 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 44 through 60 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 61 through 79 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 80 through 93 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 94 through 104 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 105 through 119 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 0 through 7 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 8 through 23 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 24 through 44 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 45 through 57 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 58 through 79 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 80 through 92 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 93 through 119 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid -1 through 33 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 34 through 53 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 54 through 58 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 59 through 79 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 80 through 93 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 94 through 118 )

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