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- PDB-2v42: Crystal structure of RseB: a sensor for periplasmic stress respon... -

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Basic information

Entry
Database: PDB / ID: 2v42
TitleCrystal structure of RseB: a sensor for periplasmic stress response in E. coli
ComponentsSIGMA-E FACTOR REGULATORY PROTEIN RSEB
KeywordsREGULATOR / REGULATORY PROTEIN / LIPOPROTEIN BINDING / SENSOR FOR PERIPLASMIC STRESS
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
MucB/RseB / MucB/RseB, N-terminal / MucB/RseB, C-terminal / MucB/RseB, C-terminal domain superfamily / MucB/RseB N-terminal domain / MucB/RseB C-terminal domain / Lipoprotein localisation LolA/LolB/LppX / outer membrane lipoprotein receptor (LolB), chain A / Clam / Mainly Beta
Similarity search - Domain/homology
ETHYL DIMETHYL AMMONIO PROPANE SULFONATE / Sigma-E factor regulatory protein RseB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.75 Å
AuthorsWollmann, P. / Zeth, K.
CitationJournal: 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
DepositionJun 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: 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 / 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGMA-E FACTOR REGULATORY PROTEIN RSEB
B: SIGMA-E FACTOR REGULATORY PROTEIN RSEB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1104
Polymers68,7202
Non-polymers3912
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint14.2 kcal/mol
Surface area33800 Å2
MethodPQS
Unit cell
Length a, b, c (Å)164.290, 164.290, 81.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYASNASN2AA28 - 887 - 67
211GLYGLYASNASN2BB28 - 887 - 67
121GLUGLULEULEU5AA89 - 12268 - 101
221GLUGLULEULEU5BB89 - 12268 - 101
131SERSERASNASN2AA123 - 191102 - 170
231SERSERASNASN2BB123 - 191102 - 170
112SERSERILEILE2AA221 - 312200 - 291
212SERSERILEILE2BB221 - 312200 - 291

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.45228, 0.89185, -0.00656), (0.88703, 0.44904, -0.10738), (-0.09283, -0.05438, -0.9942)
Vector: -72.45501, 48.2617, 53.24002)

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Components

#1: Protein SIGMA-E FACTOR REGULATORY PROTEIN RSEB / RSEB


Mass: 34359.891 Da / Num. of mol.: 2 / 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-NDS / ETHYL DIMETHYL AMMONIO PROPANE SULFONATE


Mass: 195.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 22 IS A METHIONINE WHICH WAS CLONED THERE TO HAVE A START CODON. RESIDUES 319-324 DO NOT ...RESIDUE 22 IS A METHIONINE WHICH WAS CLONED THERE TO HAVE A START CODON. RESIDUES 319-324 DO NOT MATCH THE P0AFX9 AS IT AS A HIS-TAG, NEEDED FOR PURIFICATION OF THE PROTEIN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.3 % / Description: NONE
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 2.4 M SODIUM MALONATE PH 7, 0.3 M DIMETHYLETHYLAMMONIUM PROPANE SULFONATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→2.9 Å / Num. obs: 28941 / % possible obs: 97.5 % / Observed criterion σ(I): 2.4 / Redundancy: 12.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.8
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 12 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.4 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2.75→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 24.37 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1492 5.1 %RANDOM
Rwork0.217 ---
obs0.219 27882 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 24 44 4555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224595
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9726240
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2625563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94623.091220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.09115764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2181550
X-RAY DIFFRACTIONr_chiral_restr0.0910.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023506
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.21947
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23149
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2187
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5961.52894
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04224614
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.37331880
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3724.51626
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1520tight positional0.070.05
2368tight positional0.040.05
1649medium positional0.470.5
2342medium positional0.460.5
1128loose positional0.945
1520tight thermal0.080.5
2368tight thermal0.180.5
1649medium thermal0.572
2342medium thermal0.362
1128loose thermal1.210
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 95
Rwork0.325 1952
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.64980.25240.02522.42850.04144.782-0.118-0.1434-0.0090.03540.0259-0.13690.1560.07830.0921-0.1533-0.00420.0149-0.12680.0528-0.058736.156116.91913.607
21.5309-1.71461.72757.2448-4.12574.6518-0.0498-0.173-0.1437-0.7066-0.3193-0.65250.90430.34390.36910.19490.01610.1714-0.21820.06160.040741.18389.86411.666
32.30030.4092-0.43032.1234-0.24123.4009-0.0108-0.11070.38680.0177-0.05570.3093-0.2125-0.43040.0665-0.07890.0015-0.08910.0386-0.09470.062915.618131.17430.005
48.41680.96983.43841.0850.59593.1261-0.0287-0.48530.5772-0.0619-0.43940.40820.0177-0.49810.4681-0.1812-0.05840.02540.1465-0.14550.0343-10.742123.19832.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 211
2X-RAY DIFFRACTION2A216 - 316
3X-RAY DIFFRACTION3B26 - 209
4X-RAY DIFFRACTION4B218 - 315

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