PDB-3lkl: Crystal structure of the C-terminal domain of Anti-Sigma factor a...

ID or keywords:

Entry

Database: PDB / ID: 3lkl

Title

Crystal structure of the C-terminal domain of Anti-Sigma factor antagonist STAS from Rhodobacter sphaeroides

Components

Antisigma-factor antagonist STAS

Keywords

TRANSPORT PROTEIN / MCSG / PSI /

Structural Genomics /

Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

sulfate transmembrane transporter activity / membrane => GO:0016020
Similarity search - Function

Biological species

Rhodobacter sphaeroides (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.15 Å

Authors

Nocek, B. / Marshall, N. / Davidoff, J. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of the C-terminal domain of Anti-Sigma factor antagonist STAS from Rhodobacter sphaeroides
Authors: Nocek, B. / Marshall, N. / Davidoff, J. / Freeman, L. / Joachimiak, A.

History

Deposition	Jan 27, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3lkl.cif.gz	47.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3lkl.ent.gz	39.9 KB	Display	PDB format
PDBx/mmJSON format	3lkl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lk/3lkl ftp://data.pdbj.org/pub/pdb/validation_reports/lk/3lkl	HTTPS FTP

-
Related structure data

Similar structure data	3lr1-d 4db9-5 4db9-4 6gz1-d 4ej8-d 4f7f-2 2qgv-11 3h8h-2 Search similar-shape structures by Omokage search (details) 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
Other databases	TargetDB: apc63695.3

Similar structure data

Other databases

TargetDB: apc63695.3

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (4)

Deposited unit

A: Antisigma-factor antagonist STAS

B: Antisigma-factor antagonist STAS

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

1

A: Antisigma-factor antagonist STAS

B: Antisigma-factor antagonist STAS

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

2

A: Antisigma-factor antagonist STAS

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

3

B: Antisigma-factor antagonist STAS

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

Unit cell

Length a, b, c (Å)	98.428, 98.428, 46.825
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

Details

authors state that the biological unit is unknown.

#1: Protein	Antisigma-factor antagonist STAS Mass: 11152.063 Da / Num. of mol.: 2 / Fragment: residues 391-485 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_4257 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21-DE3 / References: UniProt: Q3HKG0
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Antisigma-factor antagonist STAS

Mass: 11152.063 Da / Num. of mol.: 2 / Fragment: residues 391-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RSP_4257 / Plasmid: pMCSG19 / Production host:

Escherichia coli (E. coli) / Strain (production host): Bl21-DE3 / References: UniProt: Q3HKG0

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.1 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2 M Sodium Chloride Na/K phosphate 50% PEG 200 , pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9794 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2009 / Details: mirrors

Radiation

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

Radiation wavelength

Wavelength: 0.9794 Å / Relative weight: 1

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.963
1	1	h+k,-k,-l	2	0.037

Reflection

Resolution: 2.15→40 Å / Num. all: 14500 / Num. obs: 14242 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / B_iso Wilson estimate: 50 Å² / R_merge(I) obs: 0.094 / Net I/σ(I): 25.4

Reflection shell

Highest resolution: 2.15 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / Num. unique all: 717 / % possible all: 100

-
Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELX		model building
HKL-3000		phasing
MLPHARE		phasing
CCP4		model building
DM		model building
ARP/wARP		model building
Coot		model building
REFMAC	5.5.0102	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
CCP4		phasing
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.15→40 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.931 / SU B: 16.891 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.041 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2418	747	5.2 %	RANDOM
R_work	0.19946	-	-	-
all	0.20164	14250	-	-
obs	0.20164	13489	99.62 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 18.643 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.18 Å²	0 Å²	0 Å²
2-	-	2.18 Å²	0 Å²
3-	-	-	-4.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1395	0	0	82	1477

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.022	1415
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	936
X-RAY DIFFRACTION	r_angle_refined_deg	2.01	1.944	1912
X-RAY DIFFRACTION	r_angle_other_deg	1.086	3	2254
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.201	5	178
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.555	23.188	69
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.222	15	230
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.389	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.13	0.2	220
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1603
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	317
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.055	1.5	895
X-RAY DIFFRACTION	r_mcbond_other	0.304	1.5	367
X-RAY DIFFRACTION	r_mcangle_it	1.842	2	1423
X-RAY DIFFRACTION	r_scbond_it	3.031	3	520
X-RAY DIFFRACTION	r_scangle_it	4.72	4.5	489
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.149→2.205 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	42	-
R_work	0.199	976	-
obs	-	-	96.77 %

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	6.2209	1.5776	-6.0609	8.7137	-2.7374	1.5049	-0.2943	0.68	-0.0276	-0.7301	0.1299	-0.1339	0.5249	-0.4827	0.1644	0.2428	-0.0659	0.0491	0.2482	0.0449	0.3611	-30.944	23.7386	-7.4804
2	4.4084	0.7538	-2.694	9.5144	-4.5855	7.0406	-0.0542	-0.475	-0.2666	0.1499	-0.0487	-0.2324	0.1555	0.3678	0.103	0.2211	-0.0008	0.053	0.2179	0.0574	0.2904	-37.0113	16.8294	9.544
3	6.3541	3.8017	-8.3376	5.8249	-4.7232	6.7281	-0.4956	0.1329	-0.3902	-0.2011	0.2062	-0.3381	0.4831	0.0841	0.2894	0.2134	-0.0325	0.0022	0.2235	0.0073	0.2843	-29.596	25.1518	-2.0991
4	6.5352	3.099	-4.3358	2.8834	-2.9394	5.9615	-0.1141	0.3437	-0.089	0.0019	-0.0397	-0.0478	-0.0224	-0.1626	0.1538	0.191	-0.0302	-0.0334	0.21	0.0241	0.2543	-37.6298	29.8484	-7.4549
5	2.9365	3.8883	-3.5902	6.7201	4.4565	16.7799	-0.3846	0.0415	0.0133	0.363	0.0107	0.3847	0.4065	0.0568	0.3739	0.2343	-0.02	0.0737	0.1166	0.0319	0.3004	-43.1891	22.2823	8.5413
6	2.7004	1.1645	-3.1094	0.954	-1.9704	5.9622	0.012	0.0865	0.0009	0.1548	-0.0575	-0.1442	-0.1003	0.1681	0.0455	0.1871	-0.0476	-0.0151	0.2443	0.0308	0.2752	-27.9441	30.7158	-1.0905
7	5.3073	0.2915	-3.1959	3.1346	-1.2584	-0.3713	0.0627	0.0412	0.032	-0.0284	-0.1103	-0.0592	-0.11	-0.0734	0.0476	0.2265	-0.0532	-0.0625	0.2036	0.0317	0.2879	-37.1989	37.6502	-2.1322
8	16.0737	-2.3547	-0.8097	6.5562	-1.2088	8.4277	-0.0583	-0.0358	0.1708	0.2035	0.042	0.3365	0.0071	-0.0378	0.0163	0.1993	-0.0301	0.0154	0.1362	0.0116	0.2411	-42.009	30.2524	8.1245
9	6.3127	5.7608	-8.2634	8.8165	-2.0536	9.9855	0.1016	-0.6495	-0.02	0.1485	-0.3212	-0.3457	-0.1247	0.5397	0.2197	0.1776	-0.073	-0.0655	0.2093	0.0344	0.341	-25.3798	35.3137	2.42
10	1.6734	25.2882	10.7069	28.1849	2.6874	19.2326	0.0575	0.3457	0.9572	0.287	-0.0608	0.0983	-1.1889	0.2265	0.0033	0.474	-0.0357	0.0217	0.4459	-0.0168	0.5067	-24.1134	44.338	-4.3992
11	1.4561	-0.4906	-1.8261	4.6182	-1.4824	6.2028	0.142	-0.3239	-0.1969	0.0256	-0.0492	0.6977	-0.4521	-0.4241	-0.0929	0.1097	-0.1097	-0.0784	0.4703	-0.0852	0.4084	-45.9136	52.7648	9.5824
12	26.4129	-6.8946	-9.9263	-0.7507	7.6027	7.6519	0.1542	-0.367	-0.1407	-0.2479	-0.203	0.2815	0.2475	-0.692	0.0487	0.2017	-0.114	-0.1737	0.2906	0.0158	0.4089	-38.8596	47.1822	5.0309
13	24.5569	1.9006	12.8253	19.9338	4.0993	5.817	0.0784	1.7816	0.1657	-1.9012	-0.7259	-0.5812	-0.1793	0.509	0.6475	0.3173	-0.1314	-0.0343	0.3071	0.0368	0.3753	-29.7797	54.3646	-0.1942
14	30.3695	1.8393	0.3187	23.144	7.6799	20.979	-0.4161	1.1005	0.0122	-0.6309	0.5897	-0.0902	-1.3598	-0.3154	-0.1736	0.1613	-0.036	-0.1592	0.1459	-0.0319	0.3808	-37.1827	58.7828	3.3591
15	-0.7011	-1.8372	-3.0876	11.861	8.9433	10.5583	0.7964	0.0165	0.2725	1.2352	0.2282	0.2714	-0.9803	-0.7465	-1.0245	0.5933	0.2021	-0.0153	0.5493	-0.183	0.5993	-44.1978	63.2629	12.2634
16	6.6035	-0.2629	-4.7509	-1.2738	0.808	4.7251	0.3275	-0.3115	0.4693	0.0461	-0.0777	0.0319	-0.1781	-1.5161	-0.2498	0.1197	-0.0655	-0.0283	0.9744	-0.0928	0.3773	-42.6493	53.5714	16.6825
17	3.1966	-1.013	0.5525	-0.3809	0.8115	2.9703	0.1166	-0.2655	0.3199	-0.2894	-0.0487	-0.0363	0.0735	-0.2658	-0.0679	0.1647	-0.0921	-0.058	0.2634	-0.0539	0.2891	-31.2028	52.6475	9.4126
18	1.0939	-4.3824	-2.7448	13.0411	9.8462	4.3718	0.2354	-0.1193	0.2855	0.1887	-0.2729	0.3598	-0.0455	-0.7333	0.0375	0.25	-0.0618	0.004	0.6299	-0.0833	0.5263	-38.3299	56.5113	18.9218
19	34.8356	-18.2867	-11.0662	12.7578	5.3167	2.2219	-0.3201	-0.9398	-1.2409	0.4066	-0.1644	0.3837	1.5549	-0.4568	0.4845	0.3705	-0.3927	-0.1589	0.4903	0.124	0.3099	-30.974	41.9042	11.5847
20	18.724	-0.6998	0.7182	23.0444	-0.4153	3.0361	0.528	-0.2775	0.2962	-1.0482	0.3233	-0.0388	0.6885	-0.0851	-0.8513	0.4097	-0.0631	-0.1181	0.1297	-0.0468	0.2851	-22.3027	42.6995	8.3026

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-1 - 5
2	X-RAY DIFFRACTION	2	A	6 - 14
3	X-RAY DIFFRACTION	3	A	15 - 21
4	X-RAY DIFFRACTION	4	A	22 - 36
5	X-RAY DIFFRACTION	5	A	37 - 42
6	X-RAY DIFFRACTION	6	A	43 - 53
7	X-RAY DIFFRACTION	7	A	54 - 66
8	X-RAY DIFFRACTION	8	A	67 - 76
9	X-RAY DIFFRACTION	9	A	77 - 85
10	X-RAY DIFFRACTION	10	A	86 - 91
11	X-RAY DIFFRACTION	11	B	0 - 16
12	X-RAY DIFFRACTION	12	B	17 - 22
13	X-RAY DIFFRACTION	13	B	23 - 27
14	X-RAY DIFFRACTION	14	B	28 - 33
15	X-RAY DIFFRACTION	15	B	34 - 39
16	X-RAY DIFFRACTION	16	B	40 - 47
17	X-RAY DIFFRACTION	17	B	48 - 67
18	X-RAY DIFFRACTION	18	B	68 - 80
19	X-RAY DIFFRACTION	19	B	81 - 86
20	X-RAY DIFFRACTION	20	B	87 - 92

-
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

-
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

-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

-
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