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- PDB-2p4b: Crystal structure of E.coli RseB -

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Basic information

Entry
Database: PDB / ID: 2p4b
TitleCrystal structure of E.coli RseB
ComponentsSigma-E factor regulatory protein rseB
KeywordsSIGNALING PROTEIN / Open and closed form
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, C-terminal domain / 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 ...MucB/RseB, C-terminal domain / 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 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Sigma-E factor regulatory protein RseB
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKim, D.Y. / Kim, K.K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structure of RseB and a model of its binding mode to RseA
Authors: Kim, D.Y. / Jin, K.S. / Kwon, E. / Ree, M. / Kim, K.K.
History
DepositionMar 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: 1, 2 THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONSISTS OF THREE CHAINS (A, B, C) SEE ...BIOMOLECULE: 1, 2 THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONSISTS OF THREE CHAINS (A, B, C) SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULES. THe author state that BIOMOLECULE 1 IS A HOMODIMER AND TWO SUBUNITS ARE RELATED BY NON-CRYSTALLOGRAPIHC TWO-FOLD SYMMETRY (CHAIN A AND CHAIN B). BIOMOLECULE 2 IS A HOMODIMER AND TWO SUBUNITS ARE RELATED BY CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY (CHAIN C AND ITS EQUIVALENT).

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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
C: Sigma-E factor regulatory protein rseB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2794
Polymers99,9863
Non-polymers2921
Water5,855325
1
A: Sigma-E factor regulatory protein rseB
B: Sigma-E factor regulatory protein rseB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9503
Polymers66,6582
Non-polymers2921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-12 kcal/mol
Surface area24670 Å2
MethodPISA
2
C: Sigma-E factor regulatory protein rseB

C: Sigma-E factor regulatory protein rseB


Theoretical massNumber of molelcules
Total (without water)66,6582
Polymers66,6582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_756-x+2,y,-z+3/21
Unit cell
Length a, b, c (Å)97.683, 197.681, 108.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Sigma-E factor regulatory protein rseB


Mass: 33328.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: rseB / Plasmid: pET-22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AFX9
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 6%(w/v) PEG 8000, 0.1M HEPES, 0.1M NaCl, 5%(v/v) MPD, 5%(w/v) guanidine-HCl, 3mM b-octylglucoside, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 41505 / Num. obs: 39529 / % possible obs: 97.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.369 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2526756.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3965 10 %RANDOM
Rwork0.233 ---
obs0.233 39529 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1905 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 56.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20 Å20 Å2
2---0.97 Å20 Å2
3----1.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6447 0 20 325 6792
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it7.641.5
X-RAY DIFFRACTIONc_mcangle_it11.782
X-RAY DIFFRACTIONc_scbond_it10.322
X-RAY DIFFRACTIONc_scangle_it14.262.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.342 631 10.1 %
Rwork0.294 5643 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3bog.parambog.top

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