PDB-2v43: Crystal structure of RseB: a sensor for periplasmic stress respon...

ID or keywords:

Entry

Database: PDB / ID: 2v43

Title

Crystal structure of RseB: a sensor for periplasmic stress response in E. coli

Components

SIGMA-E FACTOR REGULATORY PROTEIN RSEB

Keywords

REGULATOR / SENSOR FOR PERIPLASMIC STRESS /

REGULATORY PROTEIN /

LIPOPROTEIN BINDING

Function / homology

Function and homology information

regulation of polysaccharide biosynthetic process / antisigma factor binding / sigma factor antagonist complex / outer membrane-bounded periplasmic space / protein stabilization / negative regulation of DNA-templated transcription /

lipid binding / identical protein binding /

plasma membrane
Similarity search - Function

Biological species

ESCHERICHIA COLI (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.37 Å

Authors

Wollmann, P. / Zeth, K.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: The Structure of Rseb: A Sensor in Periplasmic Stress Response of E. Coli.
Authors: Wollmann, P. / Zeth, K.

History

Deposition	Jun 27, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 28, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2v43.cif.gz	174.2 KB	Display	PDBx/mmCIF format
PDB format	pdb2v43.ent.gz	139.3 KB	Display	PDB format
PDBx/mmJSON format	2v43.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v4/2v43 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/2v43	HTTPS FTP

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Related structure data

Related structure data	2v42C C: citing same article (ref.)
Similar structure data	6fmu-d 3pjg-1 6fp4-d 2xb6-1 6rtj-d 1jii-1 5h52-d 1jij-1 2hau-1 5z08-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	#111 - Mar 2009 Hydrogenase similarity (1) #149 - May 2012 Leptin similarity (1)

Deposited unit

A: SIGMA-E FACTOR REGULATORY PROTEIN RSEB

B: SIGMA-E FACTOR REGULATORY PROTEIN RSEB

C: SIGMA-E FACTOR REGULATORY PROTEIN RSEB

hetero molecules

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

1

A: SIGMA-E FACTOR REGULATORY PROTEIN RSEB

B: SIGMA-E FACTOR REGULATORY PROTEIN RSEB

hetero molecules

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

2

C: SIGMA-E FACTOR REGULATORY PROTEIN RSEB

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

Unit cell

Length a, b, c (Å)	98.600, 200.700, 109.730
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-2050- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
1	2	A
2	2	B
3	2	C
1	3	A
2	3	B
3	3	C

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	ASN	ASN	2	A	A	28 - 103	7 - 82
2	1	1	GLY	GLY	ASN	ASN	2	B	B	28 - 103	7 - 82
3	1	1	GLY	GLY	ASN	ASN	2	C	C	28 - 103	7 - 82
1	2	1	GLY	GLY	ILE	ILE	6	A	A	104 - 129	83 - 108
2	2	1	GLY	GLY	ILE	ILE	6	B	B	104 - 129	83 - 108
3	2	1	GLY	GLY	ILE	ILE	6	C	C	104 - 129	83 - 108
1	1	2	SER	SER	GLN	GLN	2	A	A	130 - 192	109 - 171
2	1	2	SER	SER	GLN	GLN	2	B	B	130 - 192	109 - 171
3	1	2	SER	SER	GLN	GLN	2	C	C	130 - 192	109 - 171
1	1	3	TRP	TRP	ILE	ILE	2	A	A	222 - 312	201 - 291
2	1	3	TRP	TRP	ILE	ILE	2	B	B	222 - 312	201 - 291
3	1	3	TRP	TRP	ILE	ILE	2	C	C	222 - 312	201 - 291

NCS ensembles :

ID
1
2
3

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.4726, -0.60772, 0.63822), (-0.58787, -0.75693, -0.28544), (0.65655, -0.24029, -0.71498)	13.39288, 99.72059, 62.23261
2	given	(-0.09229, -0.83531, -0.54197), (0.84286, -0.35533, 0.40413), (-0.53015, -0.41951, 0.73685)	108.25285, -39.59167, 29.05298
3	given	(0.09195, 0.81498, 0.57215), (0.87043, -0.34485, 0.35133), (0.48363, 0.46571, -0.74109)	-10.04592, -38.37309, 25.62675

#1: Protein	SIGMA-E FACTOR REGULATORY PROTEIN RSEB / RSEB Mass: 34359.891 Da / Num. of mol.: 3 / Fragment: RESIDUES 23-318 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AFX9
#2: Chemical	ChemComp-CYS / CYSTEINE / Cysteine Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₇NO₂S
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H₂O
Compound details	SEEMS TO MODULATE THE ACTIVITY OF RPOE (SIGMA-E)
Sequence details	RESIDUE 22 IS A METHIONINE WHICH WAS CLONED THERE TO HAVE A START CODON. RESIDUES 319-324 DO NAT ...RESIDUE 22 IS A METHIONINE WHICH WAS CLONED THERE TO HAVE A START CODON. RESIDUES 319-324 DO NAT MATCH THE P0AFX9 AS IT AS A HIS-TAG, NEEDED FOR PURIFICATION OF THE PROTEIN

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.81 % / Description: NONE
Crystal grow	pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1 M TRIS-HCL PH 8.5, 25%(W/V) POLYETHYLENE GLYCOL 3350 AND 10 MM L-CYSTEINE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762
Detector	Type: ADSC CCD / Detector: CCD / Date: Sep 7, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.4→20 Å / Num. obs: 40893 / % possible obs: 95.2 % / Observed criterion σ(I): 2.4 / Redundancy: 3.7 % / R_merge(I) obs: 0.11 / Net I/σ(I): 12.6
Reflection shell	Resolution: 2.37→2.5 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / % possible all: 89.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: LARGE DOMAIN FROM P4212 DATASET

Resolution: 2.37→20 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.911 / SU B: 17.467 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.278	2205	5.1 %	RANDOM
R_work	0.228	-	-	-
obs	0.231	41422	98.5 %	-

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: 49.48 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.06 Å²	0 Å²	0 Å²
2-	-	1.73 Å²	0 Å²
3-	-	-	-0.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.37→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6456	0	28	194	6678

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	6613
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.697	1.969	8961
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	20.178	5	806
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.188	22.862	318
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.193	15	1124
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.841	15	75
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	1007
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5056
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	2623
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	4380
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	318
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	0.199	0.2	73
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.254	0.2	10
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	0.549	1.5	4199
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.953	2	6624
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.246	3	2719
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.038	4.5	2337
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	304	tight positional	0.05	0.05
1	2	B	304	tight positional	0.06	0.05
1	3	C	304	tight positional	0.06	0.05
2	1	A	252	tight positional	0.05	0.05
2	2	B	252	tight positional	0.06	0.05
2	3	C	252	tight positional	0.06	0.05
3	1	A	296	tight positional	0.06	0.05
3	2	B	296	tight positional	0.04	0.05
3	3	C	296	tight positional	0.05	0.05
1	1	A	296	medium positional	0.55	0.5
1	2	B	296	medium positional	0.61	0.5
1	3	C	296	medium positional	0.51	0.5
2	1	A	256	medium positional	0.5	0.5
2	2	B	256	medium positional	0.53	0.5
2	3	C	256	medium positional	0.41	0.5
3	1	A	274	medium positional	0.7	0.5
3	2	B	274	medium positional	0.5	0.5
3	3	C	274	medium positional	0.5	0.5
1	1	A	220	loose positional	0.56	5
1	2	B	220	loose positional	0.54	5
1	3	C	220	loose positional	0.41	5
1	1	A	304	tight thermal	0.08	0.5
1	2	B	304	tight thermal	0.08	0.5
1	3	C	304	tight thermal	0.06	0.5
2	1	A	252	tight thermal	0.1	0.5
2	2	B	252	tight thermal	0.09	0.5
2	3	C	252	tight thermal	0.07	0.5
3	1	A	296	tight thermal	0.07	0.5
3	2	B	296	tight thermal	0.06	0.5
3	3	C	296	tight thermal	0.06	0.5
1	1	A	296	medium thermal	0.58	2
1	2	B	296	medium thermal	0.59	2
1	3	C	296	medium thermal	0.61	2
2	1	A	256	medium thermal	0.76	2
2	2	B	256	medium thermal	0.77	2
2	3	C	256	medium thermal	0.68	2
3	1	A	274	medium thermal	0.55	2
3	2	B	274	medium thermal	0.51	2
3	3	C	274	medium thermal	0.48	2
1	1	A	220	loose thermal	1.82	10
1	2	B	220	loose thermal	2.04	10
1	3	C	220	loose thermal	1.75	10

LS refinement shell

Resolution: 2.37→2.43 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.39	148
R_work	0.31	2897

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	0.2554	0.3861	-0.1391	1.5636	0.2741	3.0343	0.0043	0.0276	-0.0845	0.1738	-0.0839	-0.0763	0.2586	0.0367	0.0795	-0.1565	0.0202	0.0645	-0.1531	0.0067	-0.1668	33.726	26.809	34.607
2	15.3834	0.279	-3.1777	1.31	0.2914	2.5019	-0.2161	1.0127	-0.8853	0.0756	-0.0149	0.1953	0.2082	-0.5023	0.231	-0.1949	-0.0286	0.0263	-0.0521	-0.0924	-0.0691	10.044	23.355	18.645
3	1.2002	-0.1643	-1.1392	2.2463	0.7315	2.5178	-0.0993	-0.1591	-0.0416	0.2998	0.0448	-0.2391	0.0988	0.0783	0.0546	-0.1102	0.0218	-0.0526	-0.1788	0.0145	-0.187	34.794	49.809	53.308
4	2.6964	0.2137	1.8374	5.1562	-1.5624	7.9918	-0.5808	0.587	0.5811	-0.2608	0.2666	0.1233	-0.8608	0.1187	0.3142	-0.0318	-0.1118	-0.1188	-0.0054	0.0962	-0.1735	17.95	72.285	49.041
5	4.2965	1.3238	-0.6751	2.1677	-1.196	2.604	0.1381	-0.0101	0.6003	0.1808	-0.3448	0.3357	-0.1521	-0.1776	0.2068	0.1072	0.0213	-0.0627	0.1434	-0.2438	0.2731	34.788	-6.514	29.393
6	4.9486	-0.3491	1.825	4.5908	2.674	7.0707	0.1431	-0.4261	0.198	0.0982	0.0369	0.0732	0.1867	0.0074	-0.18	-0.1523	-0.0572	0.0438	-0.0447	-0.0584	-0.1093	19.232	-30.808	24.763

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	26 - 208
2	X-RAY DIFFRACTION	2	A	221 - 314
3	X-RAY DIFFRACTION	3	B	26 - 208
4	X-RAY DIFFRACTION	4	B	220 - 314
5	X-RAY DIFFRACTION	5	C	26 - 204
6	X-RAY DIFFRACTION	6	C	219 - 316

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