PDB-4xlt: Crystal structure of response regulator receiver protein from Dya...

ID or keywords:

Entry

Database: PDB / ID: 4xlt

Title

Crystal structure of response regulator receiver protein from Dyadobacter fermentans DSM 18053

Components

Response regulator receiver protein

Keywords

SIGNALING PROTEIN / PSI-BIOLOGY / response regulator / Structural Genomics / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

phosphorelay signal transduction system
Similarity search - Function

Biological species

Dyadobacter fermentans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Chang, C. / Cuff, M. / Holowicki, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To Be Published
Title: Crystal structure of response regulator receiver protein from Dyadobacter fermentans DSM 18053
Authors: Chang, C. / Cuff, M. / Holowicki, J. / Clancy, S. / Joachimiak, A.

History

Deposition	Jan 13, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 28, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4xlt.cif.gz	68.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4xlt_validation.pdf.gz	426.4 KB	Display	wwPDB validaton report
Full document	4xlt_full_validation.pdf.gz	428.4 KB	Display
Data in XML	4xlt_validation.xml.gz	8.5 KB	Display
Data in CIF	4xlt_validation.cif.gz	10.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xl/4xlt ftp://data.pdbj.org/pub/pdb/validation_reports/xl/4xlt	HTTPS FTP

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Related structure data

Similar structure data	6dbf-d 6iev-d 4q2u-3 4nkn-2 3ie9-3 4twg-2 4ml0-3 3l10-d 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	TargetTrack: MCSG-APC103393

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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: Response regulator receiver protein

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

1

A: Response regulator receiver protein

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

Unit cell

Length a, b, c (Å)	62.945, 62.945, 69.486
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

Components on special symmetry positions

ID	Model	Components
1	1	A-229- HOH
2	1	A-234- HOH
3	1	A-257- HOH

#1: Protein	Response regulator receiver protein Mass: 15193.858 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / NS114) (bacteria) Strain: ATCC 700827 / DSM 18053 / NS114 / Gene: Dfer_0154 / Plasmid: pMCSG57 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C6VVW9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.65 Å³/Da / Density % sol: 53.55 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Sodium Acetate, 0.1M HEPES, 22% PEG4000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.97935 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 20, 2012

Radiation

Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97935 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. all: 6931 / Num. obs: 6764 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / B_iso Wilson estimate: 26.6 Å² / R_merge(I) obs: 0.058 / R_pim(I) all: 0.019 / R_rim(I) all: 0.061 / Χ²: 0.985 / Net I/av σ(I): 39.605 / Net I/σ(I): 13.9 / Num. measured all: 74878

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.3-2.32	8.5	0.665	182	0.976	0.233	0.706	1.307	97.3
2.32-2.34	9.1	0.308	168	0.986	0.105	0.326	1.062	97.7
2.34-2.36	9.5	0.305	180	0.984	0.102	0.321	0.923	98.9
2.36-2.38	9.4	0.203	155	0.992	0.067	0.214	0.967	99.4
2.38-2.4	10.3	0.22	190	0.997	0.07	0.231	0.822	99
2.4-2.43	10.2	0.157	174	0.996	0.051	0.165	1.057	100
2.43-2.45	10.5	0.199	176	0.998	0.064	0.209	0.88	100
2.45-2.48	10.6	0.193	176	0.996	0.062	0.203	0.982	100
2.48-2.5	10.7	0.176	172	0.997	0.056	0.185	0.877	100
2.5-2.53	11	0.143	186	0.998	0.045	0.15	0.821	100
2.53-2.56	11.2	0.156	158	0.995	0.049	0.163	0.94	100
2.56-2.59	11.3	0.16	198	0.997	0.05	0.168	0.896	100
2.59-2.62	11.2	0.136	171	0.998	0.043	0.143	0.894	100
2.62-2.66	11.3	0.142	166	0.996	0.045	0.149	0.927	100
2.66-2.69	11.5	0.132	171	0.997	0.041	0.138	0.945	100
2.69-2.73	11.3	0.104	178	0.998	0.032	0.109	0.972	100
2.73-2.77	11.4	0.129	180	0.997	0.04	0.135	0.896	100
2.77-2.81	11.4	0.103	173	0.999	0.032	0.108	0.996	100
2.81-2.85	11.4	0.1	172	0.997	0.031	0.104	0.923	100
2.85-2.9	11.3	0.091	184	0.998	0.029	0.096	0.942	100
2.9-2.95	11.5	0.093	176	0.998	0.029	0.098	0.876	100
2.95-3	11.3	0.082	180	0.995	0.026	0.087	0.939	100
3-3.06	11.4	0.073	177	0.997	0.023	0.077	0.92	100
3.06-3.12	11.5	0.079	176	0.997	0.025	0.082	0.971	100
3.12-3.19	11.3	0.07	169	0.998	0.022	0.074	0.942	100
3.19-3.26	11.4	0.065	179	0.999	0.02	0.068	0.959	100
3.26-3.35	11.3	0.056	188	0.999	0.018	0.059	0.954	100
3.35-3.44	11.4	0.056	164	0.996	0.018	0.059	0.995	100
3.44-3.54	11.2	0.058	179	0.998	0.018	0.061	1.216	100
3.54-3.65	9.8	0.055	152	0.999	0.019	0.059	1.558	86.4
3.65-3.78	7	0.059	68	0.995	0.022	0.063	1.416	37.6
3.78-3.93	10.8	0.058	185	0.998	0.019	0.061	1.872	100
3.93-4.11	10.5	0.046	176	0.999	0.015	0.048	1.176	97.8
4.11-4.33	11.3	0.041	166	0.999	0.013	0.043	0.807	100
4.33-4.6	11.2	0.043	180	0.999	0.014	0.045	0.818	100
4.6-4.95	11.3	0.043	185	0.999	0.014	0.045	0.827	100
4.95-5.45	11.1	0.04	178	0.997	0.013	0.042	0.767	100
5.45-6.24	11.1	0.044	179	0.997	0.014	0.046	0.773	100
6.24-7.86	10.8	0.047	190	0.998	0.015	0.049	0.958	100
7.86-50	9.3	0.05	174	0.996	0.018	0.054	1.277	93.5

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
Coot		model building
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→29.298 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 26.23 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2487	533	4.66 %	Random selection
R_work	0.1934	-	-	-
obs	0.1959	5956	83.48 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→29.298 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1000	0	0	60	1060

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	1029
X-RAY DIFFRACTION	f_angle_d	0.627	1398
X-RAY DIFFRACTION	f_dihedral_angle_d	11.955	378
X-RAY DIFFRACTION	f_chiral_restr	0.023	166
X-RAY DIFFRACTION	f_plane_restr	0.002	180

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 (%)
2.3002-2.5316	0.3162	88	0.2397	2144	X-RAY DIFFRACTION	65
2.5316-2.8976	0.2672	143	0.2274	2638	X-RAY DIFFRACTION	82
2.8976-3.6496	0.2739	167	0.2029	3090	X-RAY DIFFRACTION	95
3.6496-29.3006	0.2048	135	0.1651	3043	X-RAY DIFFRACTION	92

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	3.7811	1.8066	-0.0482	5.5436	1.2296	1.1391	0.1279	-0.3546	-0.2418	0.7931	-0.2089	1.3265	0.0673	-0.0562	0.0167	0.2315	-0.0604	0.1198	0.2541	0.087	0.4111	11.8394	7.2912	56.9037
2	6.7055	-1.6194	-2.4075	9.1661	0.5631	0.8563	-0.2176	1.1399	-0.8714	-0.9532	-0.0638	1.1894	-0.1716	-0.6698	-0.0786	0.2736	-0.1338	-0.02	0.3147	-0.0775	0.2529	16.8234	5.6146	50.0815
3	8.3961	-5.4386	0.1995	6.2011	-3.2693	7.3624	0.2088	1.5539	-0.3207	-1.5169	-0.2153	0.5863	0.699	0.4406	-0.6997	0.342	-0.0413	-0.0331	0.2849	0.1321	0.1358	20.5596	14.3628	45.4044
4	6.3159	1.0871	-1.5683	6.1405	-0.0249	3.633	-0.0923	0.1489	-0.7351	0.06	-0.1731	0.1352	0.6994	-0.1879	0.0758	0.1682	-0.0427	-0.0398	0.2007	0.0334	0.1999	24.6141	2.804	53.8689

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 50 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 64 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 65 through 76 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 77 through 129 )

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