PDB-5hl6: Crystal Structure of a Putative GAF sensor protein from Burkholde...

ID or keywords:

Entry

Database: PDB / ID: 5hl6

Title

Crystal Structure of a Putative GAF sensor protein from Burkholderia vietnamiensis

Components

Putative GAF sensor protein

Keywords

TRANSFERASE / SSGCID / Burkholderia vietnamiensi / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

Free Met sulfoxide reductase conserved site / Uncharacterized protein family UPF0067 signature. / : / GAF domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Burkholderia vietnamiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8499 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of a Putative GAF sensor protein from Burkholderia vietnamiensis
Authors: SSGCID / Dranow, D.M. / Mayclin, S.J. / Lorimer, D. / Edwards, T.E.

History

Deposition	Jan 14, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5hl6.cif.gz	140.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5hl6.ent.gz	108.8 KB	Display	PDB format
PDBx/mmJSON format	5hl6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5hl6_validation.pdf.gz	439.2 KB	Display	wwPDB validaton report
Full document	5hl6_full_validation.pdf.gz	440.5 KB	Display
Data in XML	5hl6_validation.xml.gz	15.2 KB	Display
Data in CIF	5hl6_validation.cif.gz	21.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hl/5hl6 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hl6	HTTPS FTP

-
Related structure data

Related structure data	3ksfS S: Starting model for refinement
Similar structure data	3fh9-d 7age-1 1ti7-d 3d1k-d 6s9d-d 5hzn-1 3d3s-1 2a3n-d 6bg2-3 5b3t-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-BuviA.00048.a

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (4) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (4)

Deposited unit

A: Putative GAF sensor protein

B: Putative GAF sensor protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	44.460, 70.200, 103.070
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Putative GAF sensor protein Mass: 19402.766 Da / Num. of mol.: 2 / Fragment: BuviA.00048.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria) Strain: G4 / LMG 22486 / Gene: Bcep1808_1068 / Plasmid: BuviA.00048.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JCS6
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.65 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: BuviA.00048.a.B1.PS02344 at 57.5 mg/ml was mixed 1:1 with JCSG+(c1): 20% PEG-8000, 100 mM sodium phosphate dibasic/ citric acid, pH = 4.2, 200 mM NaCl, and cryoprotected with 20% ethylene glycol

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97857 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2015 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97857 Å / Relative weight: 1

Reflection

Resolution: 1.849→50 Å / Num. obs: 28101 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / B_iso Wilson estimate: 23.23 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.058 / R_rim(I) all: 0.063 / Χ²: 0.982 / Net I/σ(I): 19.82 / Num. measured all: 164660

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.849-1.9		5.8	0.931	0.604	3.23	11855	2028	2028	0.664	100
1.9-1.95			0.96	0.454	4.25	11810	2020	2015	0.499	99.8
1.95-2.01			0.973	0.358	5.27	11532	1952	1950	0.394	99.9
2.01-2.07			0.983	0.269	6.75	11131	1888	1885	0.296	99.8
2.07-2.14			0.988	0.228	7.92	10974	1850	1849	0.251	99.9
2.14-2.21			0.991	0.175	10.29	10537	1768	1767	0.193	99.9
2.21-2.29			0.995	0.137	12.38	10203	1721	1721	0.15	100
2.29-2.39			0.995	0.122	13.8	9945	1676	1672	0.134	99.8
2.39-2.49			0.997	0.1	16.15	9507	1601	1598	0.109	99.8
2.49-2.62			0.997	0.084	19.04	9092	1534	1531	0.093	99.8
2.62-2.76			0.998	0.068	22.67	8510	1448	1442	0.075	99.6
2.76-2.93			0.998	0.057	26.17	8086	1382	1377	0.063	99.6
2.93-3.13			0.998	0.048	31.12	7579	1308	1301	0.053	99.5
3.13-3.38			0.999	0.038	37.79	7057	1222	1208	0.042	98.9
3.38-3.7			0.998	0.033	43.83	6448	1137	1124	0.037	98.9
3.7-4.14			0.999	0.03	48.11	5837	1036	1020	0.033	98.5
4.14-4.78			0.999	0.026	50.94	5028	904	887	0.029	98.1
4.78-5.85			0.999	0.024	51.14	4402	792	777	0.026	98.1
5.85-8.27			0.999	0.021	50.51	3387	624	605	0.024	97
	8.27		0.999	0.022	52.53	1740	379	344	0.024	90.8

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KSF

3ksf

Resolution: 1.8499→22.819 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.59 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2135	1387	4.94 %
R_work	0.1709	26686	-
obs	0.173	28073	99.32 %

Solvent computation

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

Displacement parameters

B_iso max: 97.08 Å² / B_iso mean: 34.3893 Å² / B_iso min: 12.3 Å²

Refinement step

Cycle: final / Resolution: 1.8499→22.819 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2367	0	12	189	2568
B_iso mean	-	-	53.01	40.05	-
Num. residues	-	-	-	-	319

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2434
X-RAY DIFFRACTION	f_angle_d	0.711	3320
X-RAY DIFFRACTION	f_chiral_restr	0.048	380
X-RAY DIFFRACTION	f_plane_restr	0.005	439
X-RAY DIFFRACTION	f_dihedral_angle_d	13.28	1436

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8499-1.916	0.2863	143	0.2214	2614	2757	100
1.916-1.9926	0.2477	115	0.1989	2643	2758	100
1.9926-2.0833	0.2575	146	0.1905	2624	2770	100
2.0833-2.193	0.2019	142	0.1777	2661	2803	100
2.193-2.3303	0.1861	128	0.1689	2659	2787	100
2.3303-2.51	0.2394	140	0.1765	2674	2814	100
2.51-2.7622	0.2132	151	0.1835	2659	2810	100
2.7622-3.161	0.2348	145	0.1818	2669	2814	100
3.161-3.9791	0.2226	135	0.1582	2703	2838	99
3.9791-22.821	0.1722	142	0.153	2780	2922	97

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	6.3949	-1.1717	5.7208	4.8155	-2.0205	7.8949	0.017	-0.0313	0.1208	-0.0248	-0.1545	-0.2846	0.1659	0.023	0.1798	0.2776	-0.0307	0.0366	0.1644	0.0093	0.203	20.8658	27.058	120.6824
2	3.2595	-2.0624	4.7973	3.9999	-1.0589	8.8364	-0.0655	0.147	-0.2063	0.125	0.0351	-0.175	-0.2081	0.4564	0.0294	0.232	-0.0111	0.0016	0.1609	0.0172	0.184	22.8771	19.5961	131.6038
3	3.4742	-2.8426	0.4522	8.7497	-1.4849	3.1476	0.0342	0.0528	0.085	-0.1393	-0.0508	0.0782	0.1041	-0.1622	0.0119	0.1434	-0.0315	0.0105	0.1122	-0.0088	0.1211	16.434	10.9123	127.8686
4	2.8677	-1.5017	-1.8033	2.3744	2.9077	3.8277	0.0143	0.1304	-0.0407	0.1125	-0.2298	0.2437	0.6797	-0.183	0.3234	0.429	-0.0481	0.0209	0.2037	-0.0027	0.2891	15.1307	0.9723	128.148
5	4.535	1.0803	1.4175	5.3495	-0.6073	4.3093	0.0936	0.2513	-0.234	-0.8217	-0.0648	-0.2944	0.617	0.0954	-0.0267	0.437	0.0009	0.0181	0.1777	-0.0369	0.1913	18.9499	4.0343	116.2252
6	9.5147	-3.7125	-0.7242	2.5989	1.36	1.0687	0.4864	-0.1893	-1.3152	-0.6619	-0.5957	1.4513	1.3555	-0.4898	-0.0515	0.7249	-0.2074	-0.1106	0.5649	-0.0338	0.5182	7.1484	2.818	116.0443
7	1.9537	-0.8179	-1.4518	0.4245	0.3786	1.7219	-0.2011	-0.0204	-0.8412	0.3973	-0.3041	0.4673	0.1077	0.1513	0.3532	0.7279	-0.3249	-0.1033	0.5071	0.0727	0.8961	5.667	5.333	123.9067
8	7.3741	-2.2568	0.9858	5.6852	0.183	4.7872	-0.1384	0.0635	-0.2211	-0.4429	0.1338	-0.2734	0.4113	0.5088	-0.0515	0.2852	0.0259	0.0781	0.1615	-0.0145	0.1741	24.0355	8.9456	119.5298
9	7.534	-0.6132	2.2636	2.4824	-0.7123	4.4543	-0.212	0.0234	-0.0714	-0.2825	0.1787	0.0756	0.1152	-0.3107	0.004	0.2346	-0.0341	-0.0121	0.1351	-0.0123	0.1697	13.2649	12.6642	120.0045
10	8.3518	0.443	5.6609	2.2263	-0.3915	7.5275	-0.1215	0.321	0.0016	-0.408	0.0356	-0.164	0.1644	0.1783	0.1005	0.3262	-0.0209	0.0875	0.1599	0.0156	0.2079	22.9344	17.9896	117.4134
11	2.0914	-0.4493	-1.0161	5.4288	4.7035	4.4461	0.5141	0.7395	-0.2852	-0.1185	0.3276	-2.9665	-0.1229	1.7373	-0.798	0.3839	0.0718	0.0512	0.5958	-0.0042	0.8111	34.9185	14.2812	128.2906
12	9.8211	4.4409	7.0752	8.2912	5.0601	5.6463	0.9447	-0.6955	-1.4695	-0.7403	0.2928	-1.0773	0.3593	-0.3706	-1.1363	0.4211	0.0001	0.0529	0.5069	0.2064	0.7405	-11.7595	11.7415	144.2527
13	5.1726	-4.824	-5.8252	6.6389	4.6153	8.5402	-0.1477	-0.3801	-0.7218	0.2172	0.0521	0.7311	0.4811	-0.5538	0.1974	0.1894	-0.0473	0.0213	0.3657	0.0236	0.308	4.8434	6.4153	148.1045
14	1.6611	0.2916	0.4235	2.972	-0.313	3.3843	-0.2138	-0.1305	0.2092	0.0837	0.066	0.0631	-0.2457	-0.0758	0.1436	0.1871	0.0265	-0.0194	0.1453	-0.0084	0.1566	17.7085	17.8055	144.4642
15	7.2398	4.3647	6.6036	6.6288	1.3854	8.3007	-0.6618	-0.1321	0.7553	-0.3605	0.9282	-0.7539	-2.4099	0.0937	-0.3936	0.6981	0.0407	-0.0328	0.4112	-0.1024	0.5279	11.386	31.667	145.1719
16	3.8448	-2.5115	1.0541	4.9772	-0.4429	2.5614	-0.1734	-0.4383	0.0511	0.2512	0.0829	0.2512	-0.1591	-0.5234	0.0817	0.2369	0.0454	0.0054	0.2458	-0.0335	0.1598	12.8267	16.4389	151.3218
17	9.1352	-6.2509	-4.5055	4.59	2.6966	5.5184	0.3541	-0.0758	-0.1656	-0.1983	0.0151	-0.4749	-0.0541	0.3059	-0.3694	0.3595	-0.0013	0.0113	0.238	-0.0185	0.2287	25.1057	1.5807	148.8676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 28 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 45 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 46 through 71 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 72 through 82 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 83 through 97 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 98 through 107 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 108 through 114 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 115 through 127 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 128 through 143 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 144 through 160 )	A
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 161 through 167 )	A
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 3 through 11 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 12 through 27 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 28 through 97 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 98 through 114 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 115 through 160 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 161 through 169 )	B

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi