PDB-6v91: Crystal structure of Stringent starvation protein A (BTH_I2974) f...

ID or keywords:

Entry

Database: PDB / ID: 6v91

Title

Crystal structure of Stringent starvation protein A (BTH_I2974) from Burkholderia thailandensis

Components

Stringent starvation protein A

Keywords

STRUCTURAL GENOMICS / SSGCID / Stringent starvation protein A / BTH_I2974 / Burkholderia thailandensis / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

Stringent starvation protein A, N-terminal / : / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutaredoxin domain profile. / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ...
Similarity search - Domain/homology

Biological species

Burkholderia thailandensis E264 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of Stringent starvation protein A (BTH_I2974) from Burkholderia thailandensis
Authors: Abendroth, J. / Davies, D.R. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Dec 12, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 15, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	6v91_validation.pdf.gz	468.2 KB	Display	wwPDB validaton report
Full document	6v91_full_validation.pdf.gz	470.4 KB	Display
Data in XML	6v91_validation.xml.gz	20.5 KB	Display
Data in CIF	6v91_validation.cif.gz	29.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v9/6v91 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/6v91	HTTPS FTP

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Related structure data

Similar structure data	6su7-1 6l8z-d 5nlm-1 6l1k-d 6l8x-d 6su7-3 6vah-d 1yy7-d 3mxm-d 6su6-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: ButhA.17888.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (9) #255 - Mar 2021 Cisplatin and DNA similarity (7)

Deposited unit

A: Stringent starvation protein A

B: Stringent starvation protein A

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	60.380, 95.640, 108.850
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Stringent starvation protein A Mass: 24736.742 Da / Num. of mol.: 2 / Fragment: ButhA.17888.a.AE1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia thailandensis E264 (bacteria) Strain: ATCC 700388 / DSM 13276 / CIP 106301 / E264 / Gene: BTH_I2974 / Plasmid: ButhA.17888.a.AE1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q2SUC1
#2: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 307 / 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: 3.2 Å³/Da / Density % sol: 61.6 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: For native data collection: Anatrace Morpheus screen G7: 20mM of each Sodium formate, Ammonium acetate, Sodium citrate tribasic dihydrate, Sodium potassium tartrate tetrahydrate, Sodium ...Details: For native data collection: Anatrace Morpheus screen G7: 20mM of each Sodium formate, Ammonium acetate, Sodium citrate tribasic dihydrate, Sodium potassium tartrate tetrahydrate, Sodium oxamate: 100mM Na-HEPES / MOPS acid pH 7.5: 40% (V/V) Glycerol, 20% (w/V) PEG 4000: ButhA.17888.a.AE1 (labled as CrpaA.01056.a.AE1.PW38685) at 30.5mg/ml: 311984 g7: cryo: direct: puck ocs5-5. For phasing, a crystal from the same tray, condition H9 (20mM of each L-Na-Glutamate, Alanine (racemic), Glycine, Lysine HCl (racemic), Serine (racemic): 100mM Tris base / Bicine pH 8.5: 40% (v/v) PEG 500 MME, 20% (w/V) PEG 20000) was incubated for 30sec in a mix of 90% reservoir and 10% 5M NaI in ethylene glycol and vitrified without further cryoprotection. 360deg of data were collected in-house at Cu-Ka radiation.Tray: 311984 h9, puck ocs5-14.

Crystal

Density Matthews: 3.2 Å³/Da / Density % sol: 61.6 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop
Details: For native data collection: Anatrace Morpheus screen G7: 20mM of each Sodium formate, Ammonium acetate, Sodium citrate tribasic dihydrate, Sodium potassium tartrate tetrahydrate, Sodium ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F		1	0.97872
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
RAYONIX MX-300	1	CCD	Nov 21, 2019
RIGAKU SATURN 944+	2	CCD	Nov 22, 2019

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	C(111)	SINGLE WAVELENGTH	M	x-ray	1
2		SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	1.5418	1

Reflection

Resolution: 1.9→50 Å / Num. obs: 50160 / % possible obs: 99.5 % / Redundancy: 5.952 % / B_iso Wilson estimate: 40.249 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.047 / R_rim(I) all: 0.051 / Χ²: 1.041 / Net I/σ(I): 19.65

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
1.9-1.95	6.006	0.52	3.58	3608	0.909	0.57	96.9
1.95-2	6.197	0.417	4.04	3533	0.936	0.455	100
2-2.06	6.161	0.311	5.44	3492	0.96	0.34	99.9
2.06-2.12	6.172	0.24	7.1	3384	0.972	0.262	99.9
2.12-2.19	6.121	0.188	8.86	3293	0.983	0.205	99.9
2.19-2.27	5.697	0.181	10.32	3140	0.981	0.2	98.1
2.27-2.36	6.078	0.125	13.01	3058	0.992	0.137	99.5
2.36-2.45	6.057	0.095	16.23	2972	0.995	0.104	99.8
2.45-2.56	5.976	0.078	19.55	2818	0.996	0.086	99.9
2.56-2.69	5.966	0.068	22.07	2725	0.997	0.074	99.8
2.69-2.83	5.92	0.059	25.36	2608	0.997	0.064	99.8
2.83-3	5.904	0.051	29.56	2466	0.998	0.056	99.7
3-3.21	5.837	0.046	32.41	2328	0.998	0.05	99.9
3.21-3.47	5.784	0.04	37	2164	0.998	0.043	99.9
3.47-3.8	5.745	0.037	39.19	2014	0.999	0.04	99.9
3.8-4.25	5.774	0.033	41.33	1822	0.999	0.036	100
4.25-4.91	5.784	0.03	42.89	1626	0.999	0.033	100
4.91-6.01	5.795	0.028	42.91	1402	0.999	0.03	100
6.01-8.5	5.661	0.026	42.92	1093	0.999	0.029	100
8.5-50	4.795	0.027	40.62	614	0.998	0.031	94.5

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→33.92 Å / SU ML: 0.2194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2223

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2149	2022	4.03 %	0
R_work	0.174	-	-	-
obs	0.1756	50149	99.46 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 49.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→33.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3298	0	35	307	3640

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0068	3493
X-RAY DIFFRACTION	f_angle_d	0.852	4740
X-RAY DIFFRACTION	f_chiral_restr	0.0532	521
X-RAY DIFFRACTION	f_plane_restr	0.0058	624
X-RAY DIFFRACTION	f_dihedral_angle_d	20.4957	1326

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 (%)
1.9-1.95	0.4909	127	0.4451	3338	X-RAY DIFFRACTION	96.65
1.95-2	0.2793	144	0.2364	3359	X-RAY DIFFRACTION	100
2-2.06	0.256	142	0.2013	3421	X-RAY DIFFRACTION	99.94
2.06-2.13	0.2442	140	0.1845	3400	X-RAY DIFFRACTION	99.94
2.13-2.2	0.2319	129	0.1836	3439	X-RAY DIFFRACTION	99.97
2.2-2.29	0.3453	140	0.265	3341	X-RAY DIFFRACTION	97.95
2.29-2.39	0.2284	146	0.1829	3438	X-RAY DIFFRACTION	99.72
2.39-2.52	0.2219	161	0.1726	3415	X-RAY DIFFRACTION	99.78
2.52-2.68	0.1868	133	0.1713	3420	X-RAY DIFFRACTION	99.83
2.68-2.88	0.2249	146	0.1785	3456	X-RAY DIFFRACTION	99.81
2.88-3.17	0.2108	173	0.1717	3435	X-RAY DIFFRACTION	99.75
3.17-3.63	0.2089	135	0.1568	3490	X-RAY DIFFRACTION	99.92
3.63-4.58	0.1659	140	0.1423	3536	X-RAY DIFFRACTION	99.95
4.58-33.92	0.2014	166	0.1591	3639	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	3.03540488101	0.458631930988	0.514579761017	4.48755121155	0.616531418726	4.63818881049	0.0978361502371	-0.304314623355	-0.102016112852	0.362508862398	-0.0190053807038	0.28849729321	0.340375990473	-0.284532867023	-0.0599432636567	0.220980710795	-0.00255364319136	0.0165617362298	0.22378983852	0.0359762531194	0.242531321479	23.8276959982	61.5629646436	15.6330756012
2	4.50756460522	-0.0279070269892	-0.283711822456	3.74371025846	2.33877357043	4.04081182692	0.0472354593506	-0.464151828729	-0.135887229577	0.178040112477	0.193909085064	-0.293263688689	0.209091109284	0.271693148392	-0.199004018609	0.327472031861	0.0378919146647	-0.0297179609952	0.291781316548	0.113393788433	0.261378269352	40.1330982209	64.2701891349	12.7740348218
3	3.49629954574	0.683820512564	0.550113192015	3.78552778963	2.86883378538	2.2332835463	0.0845718908271	-0.605511768579	0.196214959716	0.422289363471	0.170721273999	-0.383303120277	0.139375831133	0.660663685447	-0.278960281971	0.223482144592	-0.0197980462402	-0.0367999683856	0.342462949052	-0.053032488357	0.299055908594	45.2888582685	75.846109201	11.7174461763
4	4.71019366162	5.07696741306	-4.96368583193	8.92343464456	-5.8335701484	5.29225882404	-0.447596451927	0.735035418174	-0.195490738839	-0.423789013011	0.554154821736	-0.00482501537213	0.077827403328	-0.239477355706	-0.0306754349594	0.317987260946	-0.0182646113636	-0.00772368015647	0.336746912141	-0.019921750999	0.257065519027	34.5991497067	66.8054797336	-3.57506377602
5	4.51752102899	-0.279966724084	-1.03744464144	1.66989880566	0.0693425300826	2.49867444489	0.0474297124612	-0.130617658971	0.374277073868	-0.0174858625911	0.0487360253747	0.0543313424525	-0.149430927627	0.115144197781	-0.105507867467	0.212803189014	0.0137226033328	-0.00912949477526	0.181176335554	0.00102000531035	0.203914784659	32.5446694454	76.5467847656	7.1937119312
6	5.44569566499	-6.40544140319	1.98823568374	7.67106061007	-2.15372277802	2.74740198139	-0.91148448435	0.32358610332	1.40752171024	0.521437932021	0.871031443827	-1.14791424229	-1.77261560261	0.390864899157	-0.0895470109595	0.778210391914	-0.143923889792	-0.107435750089	0.635881782022	0.174821541791	1.16830047231	25.6676121392	84.4498494773	4.00725859549
7	4.36877492518	1.32414277985	-0.187770093213	5.16307218912	0.900648060043	0.946996232321	-0.298997839038	-0.111448425676	-0.651612886362	-0.79591258361	-0.209451012881	-1.43659926319	0.214450320141	0.610544067228	0.450579165103	0.476578349076	0.108063875602	0.230973284039	0.421875239136	0.254453754676	0.78769897071	51.011320097	42.3700025291	10.5326246326
8	5.08911636048	4.80383466418	-1.14723887559	4.61146681357	-1.32078982708	0.904744760418	-0.676447176763	0.168454331513	-1.11492736939	-0.571793968597	0.217150562793	-1.46600296287	0.107036868716	0.845111288474	0.370190114909	0.676128074429	0.17592017281	0.295907364535	0.848577974182	0.245007088769	1.11770687526	58.3687623277	47.5454533619	5.22787209463
9	8.14821096472	4.98872437475	-0.480065700523	6.36269418726	-1.36591128691	2.2200583047	-0.506370030197	-0.0070614203816	-0.177570190235	-1.02753738859	-0.0120895622227	-0.872830780513	-0.0937458813145	0.242944821378	0.54682768863	0.555849416792	0.0797071736911	0.146132862383	0.318280985879	0.14933389667	0.556250662463	47.2566924954	50.601113251	5.88365170564
10	2.75311232282	3.05544437661	-3.34731427958	7.70626332663	-0.932524652973	6.08076383483	-0.719107596169	0.469345709426	-0.400655949021	-1.30242260313	-0.019164496876	-0.350952430941	0.388524120598	-0.631085066214	0.574913752585	0.563006567255	0.0223805180729	0.065118755842	0.380719871281	-0.0560688355529	0.445854378513	33.9793971917	39.572320924	7.89935674643
11	6.66276742305	4.92217005649	3.33047500685	7.29845031285	2.46347267958	4.83373276349	0.555978089282	-0.107265982867	-0.605153860647	0.2190898484	-0.275726148243	-0.587122763573	0.241685082533	0.176823571773	-0.28391727825	0.363832794917	0.026024769444	-0.0397482690131	0.291444340292	0.121475696376	0.369969122012	32.8781159165	49.323213793	18.3332696977
12	2.20211599916	-1.50622095047	-3.33833189038	2.1360981702	0.766532917353	7.09562431983	0.121607868829	-0.328384328057	0.65514082251	0.194868168462	-0.239089070601	-1.69991084355	-0.46423465919	1.01440975604	0.155106992421	0.534029562514	-0.143471443743	-0.163366210063	0.542739382443	0.244558852525	0.989961928565	53.0783725517	54.223425696	25.8825933296
13	6.99513801293	4.41719113299	0.0367419935892	4.49795818307	1.1670977123	0.829257779276	0.61844779161	-0.656866842806	0.394498694458	1.19720688339	-0.855136452831	-0.681495779443	-0.559671221338	0.805046516412	0.129273605174	0.563747966546	-0.250785407259	-0.192114121373	0.573201425511	0.199032517199	0.597764289834	44.5584976244	47.9527825212	33.1169417524
14	5.81876751667	0.831076064913	-1.22979255233	5.48383858643	-2.8730525401	6.37479336713	-0.0264963903868	0.0777213620714	-0.256677386772	-0.458811876668	-0.108247378999	-0.219397176648	0.768214785394	-0.119450680884	0.161536198983	0.379617078317	0.0136289855124	0.00461593752078	0.319115679653	0.111509256017	0.361296664748	33.8908428556	35.6425029803	21.315880044
15	5.32426805018	0.872982943964	1.3985015003	2.96931353583	-0.24735979321	2.49210731675	0.301809172497	-0.493080186722	0.00912444037802	0.351065955385	-0.739540696373	-1.09673572363	0.249740260789	0.450478126973	0.401140581627	0.359528572381	-0.0350261095889	-0.0909490413088	0.4741401875	0.32848472837	0.791977655902	48.2935557403	42.2729918685	26.1153413187
16	5.01979932799	0.0740335461728	-1.27167169139	4.22292319909	-1.60839868221	2.45912982224	0.284829032728	-0.474272321631	-0.419304562803	0.512246344585	-0.410059654651	-0.789181940352	0.409203151271	0.397334211863	0.30019392407	0.371180370248	-0.118665085044	-0.0639860078339	0.460896631695	0.316261666988	0.643614439424	42.4148703329	35.1488665035	29.6322213293
17	5.18931681898	0.681477806137	0.442521297225	2.2137864886	1.48862563004	1.00527103537	-0.0485822978932	-0.294562991391	-0.472112197715	0.286447744135	-0.425263851889	-1.15389097713	0.578509311611	0.690077696083	-0.138587881283	0.408169822567	0.28363111577	0.131751836807	0.526892267307	0.500505444288	1.25047597578	53.3498732989	34.2330988302	18.5801307772

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 83 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 84 through 113 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 114 through 140 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 141 through 150 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 151 through 201 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 202 through 211 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 23 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 24 through 44 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 45 through 73 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 74 through 83 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 84 through 100 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 101 through 115 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 116 through 139 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 140 through 150 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 151 through 171 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 172 through 185 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 186 through 202 )

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