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- PDB-3m4w: Structural basis for the negative regulation of bacterial stress ... -

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Basic information

Entry
Database: PDB / ID: 3m4w
TitleStructural basis for the negative regulation of bacterial stress response by RseB
Components
  • Sigma-E factor negative regulatory protein
  • Sigma-E factor regulatory protein rseB
KeywordsSignaling Protein/Signaling Protein / RseA / RseB / RseP / stress response / sigma factor / Periplasm / Cell membrane / Transmembrane / Signaling Protein-Signaling Protein complex
Function / homology
Function and homology information


regulation of polysaccharide biosynthetic process / antisigma factor binding / sigma factor antagonist activity / sigma factor antagonist complex / outer membrane-bounded periplasmic space / molecular adaptor activity / protein stabilization / negative regulation of DNA-templated transcription / lipid binding / identical protein binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3960 / Sigma-E factor negative regulatory protein RseA / Anti sigma-E protein RseA, N-terminal / Anti sigma-E protein RseA, C-terminal / MucB/RseB / MucB/RseB, N-terminal / MucB/RseB, C-terminal / Anti sigma-E protein RseA, N-terminal domain superfamily / MucB/RseB, C-terminal domain superfamily / Anti sigma-E protein RseA, N-terminal domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3960 / Sigma-E factor negative regulatory protein RseA / Anti sigma-E protein RseA, N-terminal / Anti sigma-E protein RseA, C-terminal / MucB/RseB / MucB/RseB, N-terminal / MucB/RseB, C-terminal / Anti sigma-E protein RseA, N-terminal domain superfamily / MucB/RseB, C-terminal domain superfamily / Anti sigma-E protein RseA, N-terminal domain / Anti sigma-E protein RseA, C-terminal domain / MucB/RseB N-terminal domain / MucB/RseB C-terminal domain / Lipoprotein localisation LolA/LolB/LppX / outer membrane lipoprotein receptor (LolB), chain A / Clam / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Anti-sigma-E factor RseA / Sigma-E factor regulatory protein RseB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKim, D.Y. / Kwon, E. / Choi, J.K. / Hwang, H.-Y. / Kim, K.K.
CitationJournal: Protein Sci. / Year: 2010
Title: Structural basis for the negative regulation of bacterial stress response by RseB
Authors: Kim, D.Y. / Kwon, E. / Choi, J.K. / Hwang, H.-Y. / Kim, K.K.
History
DepositionMar 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
D: Sigma-E factor regulatory protein rseB
E: Sigma-E factor negative regulatory protein
F: Sigma-E factor negative regulatory protein
G: Sigma-E factor negative regulatory protein
H: Sigma-E factor negative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,58214
Polymers176,1908
Non-polymers3926
Water7,584421
1
A: Sigma-E factor regulatory protein rseB
C: Sigma-E factor regulatory protein rseB
E: Sigma-E factor negative regulatory protein
G: Sigma-E factor negative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2917
Polymers88,0954
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10680 Å2
ΔGint-38 kcal/mol
Surface area27260 Å2
MethodPISA
2
B: Sigma-E factor regulatory protein rseB
D: Sigma-E factor regulatory protein rseB
F: Sigma-E factor negative regulatory protein
H: Sigma-E factor negative regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2917
Polymers88,0954
Non-polymers1963
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-40 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.097, 119.513, 150.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Sigma-E factor regulatory protein rseB


Mass: 33328.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: RseB (Amino Acids 24-318) / Plasmid: PET-22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AFX9
#2: Protein
Sigma-E factor negative regulatory protein / Sigma-E factor negative regulatory protein RseA


Mass: 10718.712 Da / Num. of mol.: 4 / Fragment: residues 121-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: RseA (Amino Acids 121-216) / Plasmid: PET-22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AFX7
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 287 K / Method: microbatch, under oil / pH: 6.5
Details: 28% PEG 550MME, 10mM ZnSO4, 100mM MES, pH 6.5, Microbatch, under oil, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 71675 / Num. obs: 69381 / % possible obs: 96.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 30.2 Å2 / Rsym value: 0.062 / Net I/σ(I): 34.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.95 / Num. unique all: 6632 / Rsym value: 0.368 / % possible all: 94.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P4B

2p4b


Resolution: 2.3→19.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2853301.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3325 5 %RANDOM
Rwork0.239 ---
obs0.239 66103 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5512 Å2 / ksol: 0.332924 e/Å3
Displacement parametersBiso mean: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2---6.75 Å20 Å2
3---6.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10108 0 6 421 10535
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 524 5 %
Rwork0.267 9882 -
obs--90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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