PDB-7ltq: Crystal Structure of a histidine kinase from Burkholderia ambifar...

ID or keywords:

Entry

Database: PDB / ID: 7ltq

Title

Crystal Structure of a histidine kinase from Burkholderia ambifaria MC40-6

Components

Histidine kinase

Keywords

TRANSFERASE / SSGCID / Histidine kinase / Burkholderia ambifaria / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

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

Biological species

Burkholderia ambifaria (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of a histidine kinase from Burkholderia ambifaria MC40-6
Authors: Abendroth, J. / Yano, J.K. / Sankaran, B. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Feb 19, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 17, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ltq.cif.gz	472.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7ltq.ent.gz	323.7 KB	Display	PDB format
PDBx/mmJSON format	7ltq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ltq_validation.pdf.gz	485.6 KB	Display	wwPDB validaton report
Full document	7ltq_full_validation.pdf.gz	492.4 KB	Display
Data in XML	7ltq_validation.xml.gz	40.9 KB	Display
Data in CIF	7ltq_validation.cif.gz	59.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lt/7ltq ftp://data.pdbj.org/pub/pdb/validation_reports/lt/7ltq	HTTPS FTP

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Related structure data

Related structure data	6nb0S S: Starting model for refinement
Similar structure data	1uxp-d 3fdd-d 6axg-1 6ar3-1 6axg-4 6axg-6 3h87-d 6ar1-1 1hlu-d 1ky8-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 (6) #183 - Mar 2015 Phototropin similarity (6) #104 - Aug 2008 Selenocysteine Synthase similarity (1)

Deposited unit

A: Histidine kinase

B: Histidine kinase

C: Histidine kinase

D: Histidine kinase

hetero molecules

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

1

A: Histidine kinase

C: Histidine kinase

hetero molecules

defined by author&software
Evidence: gel filtration
60.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Histidine kinase

D: Histidine kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	95.870, 95.870, 205.020
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

Components on special symmetry positions

ID	Model	Components
1	1	C-476- HOH

#1: Protein	Histidine kinase Mass: 29846.904 Da / Num. of mol.: 4 / Fragment: BuamA.00863.e.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia ambifaria (strain MC40-6) (bacteria) Strain: MC40-6 / Gene: BamMC406_3749 / Plasmid: BuamA.00863.e.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1Z136
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CO / COBALT (II) ION Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.1 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Hampton Research Crystal Screen HT condition G1: 1.8M ammonium sulfate, 100mM MES monhydrate pH 6.5, 10mM Cobalt (II) chloride: BuamA.00863.e.A1.PS01103 at 28.3mg/ml: tray 223322 g1: cryo: ...Details: Hampton Research Crystal Screen HT condition G1: 1.8M ammonium sulfate, 100mM MES monhydrate pH 6.5, 10mM Cobalt (II) chloride: BuamA.00863.e.A1.PS01103 at 28.3mg/ml: tray 223322 g1: cryo: likely 25% EG: puck aog4-2.

Crystal

Density Matthews: 2.28 Å³/Da / Density % sol: 46.1 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Hampton Research Crystal Screen HT condition G1: 1.8M ammonium sulfate, 100mM MES monhydrate pH 6.5, 10mM Cobalt (II) chloride: BuamA.00863.e.A1.PS01103 at 28.3mg/ml: tray 223322 g1: cryo: ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 11, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9774 Å / Relative weight: 1

Reflection

Resolution: 2.15→50 Å / Num. obs: 60058 / % possible obs: 99.6 % / Redundancy: 6.904 % / B_iso Wilson estimate: 39.102 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.073 / R_rim(I) all: 0.079 / Χ²: 0.897 / Net I/σ(I): 19.11

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.15-2.21	6.658	0.588	3.01	4403	0.915	0.639	99.8
2.21-2.27	6.893	0.485	3.75	4251	0.933	0.526	99.7
2.27-2.33	7.126	0.383	4.85	4184	0.956	0.413	99.9
2.33-2.4	7.109	0.314	5.86	4079	0.972	0.339	100
2.4-2.48	7.09	0.254	7.28	3909	0.979	0.275	100
2.48-2.57	7.101	0.219	8.45	3790	0.982	0.237	99.9
2.57-2.67	7.06	0.183	9.84	3688	0.988	0.198	99.9
2.67-2.78	7.028	0.148	12.27	3515	0.992	0.16	99.8
2.78-2.9	7.082	0.126	14.58	3421	0.993	0.136	100
2.9-3.04	7.04	0.101	17.75	3222	0.996	0.109	99.9
3.04-3.21	6.973	0.075	23.14	3140	0.997	0.081	99.9
3.21-3.4	6.937	0.059	28.58	2937	0.998	0.064	99.9
3.4-3.63	6.755	0.047	34.38	2767	0.998	0.051	99.7
3.63-3.93	6.619	0.041	39.33	2581	0.999	0.044	99.8
3.93-4.3	6.737	0.036	43.47	2408	0.999	0.039	99.9
4.3-4.81	6.606	0.033	47.41	2195	0.999	0.036	99.7
4.81-5.55	6.57	0.034	44.61	1921	0.999	0.037	99.5
5.55-6.8	6.517	0.036	42.53	1663	0.999	0.039	99.5
6.8-9.62	6.535	0.028	53.63	1311	0.999	0.03	99.5
9.62-50	6.155	0.026	57.4	673	0.999	0.028	84.9

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19	refinement
PDB_EXTRACT	3.27	data extraction
MR-Rosetta		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: MR-rosetta starting from pdb entry 6NB0

6nb0

Resolution: 2.15→19.9 Å / SU ML: 0.2477 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2255	1956	3.26 %	0
R_work	0.1682	58026	-	-
obs	0.1701	59982	99.8 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 39.34 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→19.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7313	0	39	550	7902

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0064	7597
X-RAY DIFFRACTION	f_angle_d	0.7972	10431
X-RAY DIFFRACTION	f_chiral_restr	0.0439	1277
X-RAY DIFFRACTION	f_plane_restr	0.0068	1363
X-RAY DIFFRACTION	f_dihedral_angle_d	12.7575	2639

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 (%)
2.15-2.2	0.3277	132	0.224	4091	X-RAY DIFFRACTION	99.67
2.2-2.26	0.256	186	0.2174	4055	X-RAY DIFFRACTION	99.69
2.26-2.33	0.2367	145	0.2009	4072	X-RAY DIFFRACTION	99.88
2.33-2.4	0.2978	141	0.1888	4101	X-RAY DIFFRACTION	100
2.4-2.49	0.228	126	0.1841	4108	X-RAY DIFFRACTION	100
2.49-2.59	0.2213	108	0.1737	4168	X-RAY DIFFRACTION	99.93
2.59-2.71	0.2679	151	0.1919	4057	X-RAY DIFFRACTION	99.79
2.71-2.85	0.2649	148	0.1729	4131	X-RAY DIFFRACTION	99.93
2.85-3.03	0.242	152	0.1886	4110	X-RAY DIFFRACTION	99.93
3.03-3.26	0.2444	127	0.1676	4173	X-RAY DIFFRACTION	99.93
3.26-3.59	0.2233	131	0.1635	4152	X-RAY DIFFRACTION	99.84
3.59-4.1	0.1923	115	0.144	4210	X-RAY DIFFRACTION	99.79
4.1-5.15	0.1831	154	0.1408	4218	X-RAY DIFFRACTION	99.68
5.15-19.9	0.2039	140	0.1665	4380	X-RAY DIFFRACTION	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	0.701832754213	0.0235283363197	-0.596709441828	0.854843961925	-0.723503999414	3.16029307963	0.00886775914784	-0.00733828932669	0.0403070089939	0.00256713448176	-0.0190635810173	0.0593834603811	-0.245046746667	0.0455270388848	0.0138122988542	0.152070835767	0.000653621918547	-0.0460726057907	0.257633527187	-0.00921335908683	0.203892071557	11.6750509353	53.3570430007	80.7986936711
2	3.07922866874	-0.515544643512	-1.4872812798	5.05985469916	1.90721717036	3.99436339456	0.151024270877	-0.297907860465	-0.114390363057	0.247746954413	-0.298603270877	0.166403854574	0.473642019127	-0.210613411829	0.122913045996	0.304946774311	-0.0728764209273	-0.0305390911995	0.316897732486	0.0149016836142	0.165950099363	8.28330711664	46.6406451105	71.1031625106
3	1.03530534073	-0.53876591298	-0.0772667510248	2.83208502748	1.69599479973	1.48769462001	0.0455723429285	0.331692636812	-0.0718705615156	-0.546676025306	-0.0115956267881	-0.0850383394029	-0.417318721583	-0.179767697506	0.023794244613	0.257988389477	-0.0351927495217	-0.0193433883143	0.446188490312	-0.019655017863	0.23745163085	-11.4518270507	51.2797002189	79.9019734238
4	1.84256869599	-0.0881922456918	-0.677693032701	4.15159049102	-1.12022303593	3.22590335484	0.000185534314846	0.0149010738903	-0.00435080807707	0.126144829292	-0.180554201863	-0.148840502616	-0.100589412991	0.00974522166041	0.141753159643	0.158497409963	-0.0124958218342	-0.0221679193696	0.322138518287	0.014888559239	0.168674581041	-8.31139514438	52.5150270697	106.173946778
5	2.2014370907	1.91017837141	-2.83990036211	3.6566559999	-4.24575598176	7.00761859707	-0.0885485970489	-0.207852372663	-0.15601311643	-0.102432088856	-0.145569680162	-0.124197940072	0.23806668686	0.293236957293	0.207505077084	0.148811204245	-0.00218577122577	-0.00455673496149	0.236311980439	-0.0551038750866	0.21789536911	21.610535868	53.4143042829	90.1957874068
6	5.11082609364	2.13393689634	-1.41336717842	7.74738759708	-3.39879672256	5.51453070266	-0.270727146453	-0.434584123011	-0.980923652399	0.02347721429	-0.316803401452	-0.169227127444	0.98578377947	0.57011469722	0.529136299751	0.340685073267	0.103234538312	0.0528143165672	0.248938926328	0.0359790599368	0.35066812423	11.3336043675	35.4826842267	105.455746231
7	5.01553482225	3.48599817156	-5.2421536484	2.64171578281	-3.87566251002	5.72353091698	-1.55218066892	1.05625282632	-1.21849550255	-0.672384935644	0.306000412462	-0.621195862602	2.34583207894	-0.744127647373	1.21329526693	0.611642021545	-0.0790560597248	0.135375140435	0.621871909747	-0.0730595399297	0.359875310158	29.2910052777	47.8217741912	82.3842541921
8	2.58671627071	0.0704442787856	-0.408207729007	3.57258805133	0.950076230998	3.65155224592	-0.0993787108982	0.138980151728	0.169431420479	-0.274663873819	0.139459180976	-0.197687266221	-0.208379652309	0.43140223497	-0.0197639802989	0.178411953569	-0.0476753864651	-0.00208553318757	0.253793050298	0.00264032289147	0.195083273324	33.7057763432	69.531809986	81.493533885
9	1.92257507922	-1.57097373541	-1.8517504263	4.0411028799	3.16732393926	4.39822235785	0.00578635693926	0.603012678	-0.247221951946	-0.188313066217	0.0851377651169	0.117624067838	0.0405562241299	-0.0351740114542	-0.0648483499814	0.195644800668	-0.0376850965615	-0.0440857911676	0.626598173433	0.0193683431708	0.33692717656	-20.8952239841	53.2378122377	82.4530161309
10	2.91476215359	-1.01319868263	1.32743332051	4.23938280062	-1.11953041394	0.716216769076	0.140984683996	0.321484975145	-1.26094396595	-0.241800668551	-0.534990820249	0.296358687032	0.757912061977	-0.922155086064	0.26846422332	0.416724431664	-0.235732975248	0.107200996016	0.531891684003	-0.175589698835	0.649550240013	-11.2928459922	34.764580924	69.9495954228
11	4.14937335301	-4.82491234112	-4.19880246599	6.00373431292	4.74857342986	4.29299814057	-1.08064677905	-0.0358017590785	-1.52213822725	0.93795361323	-0.261544146535	0.718725890814	0.850148689339	1.14060970885	1.3814538827	0.398471933041	0.0241593572504	0.164302421129	0.824405393736	0.0755397590838	0.501359487796	-29.2533073419	48.5204752498	91.5642581914
12	1.81097772034	0.266799356527	-0.447551609422	3.39619214591	-0.693099213583	4.55726603095	-0.0808484744852	0.18331278414	0.0954521759223	0.149887586274	-0.0490431038389	0.0502828956124	-0.250145575484	-0.0422176542953	0.11484628754	0.166133561509	0.0245090456947	-0.0109999870406	0.331994087914	0.072363716632	0.236228197276	-32.6272334035	70.0715692033	89.3961005409

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 161 )	A	A	3 - 161	1 - 159
2	2	chain 'A' and (resid 162 through 258 )	A	A	162 - 258	160 - 256
3	3	chain 'B' and (resid 7 through 102 )	B	E	7 - 102	1 - 96
4	4	chain 'B' and (resid 103 through 258 )	B	E	103 - 258	97 - 248
5	5	chain 'C' and (resid 7 through 59 )	C	I	7 - 59	1 - 53
6	6	chain 'C' and (resid 60 through 87 )	C	I	60 - 87	54 - 81
7	7	chain 'C' and (resid 88 through 102 )	C	I	88 - 102	82 - 96
8	8	chain 'C' and (resid 103 through 256 )	C	I	103 - 256	97 - 250
9	9	chain 'D' and (resid 8 through 58 )	D	L	8 - 58	1 - 51
10	10	chain 'D' and (resid 59 through 88 )	D	L	59 - 88	52 - 81
11	11	chain 'D' and (resid 89 through 102 )	D	L	89 - 102	82 - 95
12	12	chain 'D' and (resid 103 through 256 )	D	L	103 - 256	96 - 249

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