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- PDB-2z2s: Crystal Structure of Rhodobacter sphaeroides SigE in complex with... -

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Basic information

Entry
Database: PDB / ID: 2z2s
TitleCrystal Structure of Rhodobacter sphaeroides SigE in complex with the anti-sigma ChrR
Components
  • Anti-Sigma factor ChrR, transcriptional activator ChrR
  • RpoE, ECF SigE
KeywordsTRANSCRIPTION / ECF sigma factor / anti-sigma factor / cupin fold / DNA-binding / Transcription regulation / Activator / Metal-binding / Zinc binding transcription factor
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / metal ion binding
Similarity search - Function
Anti-sigma factor ChrR, putative / Anti-sigma factor, zinc-finger domain / ChrR-like cupin domain / Anti-sigma factor, zinc-finger domain superfamily / ChrR Cupin-like domain / Putative zinc-finger / Putative zinc-finger / RNA polymerase sigma-70 like / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 ...Anti-sigma factor ChrR, putative / Anti-sigma factor, zinc-finger domain / ChrR-like cupin domain / Anti-sigma factor, zinc-finger domain superfamily / ChrR Cupin-like domain / Putative zinc-finger / Putative zinc-finger / RNA polymerase sigma-70 like / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Arc Repressor Mutant, subunit A / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Anti-sigma-E factor ChrR / ECF RNA polymerase sigma factor RpoE
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDarst, S.A. / Campbell, E.A.
CitationJournal: Mol.Cell / Year: 2007
Title: A conserved structural module regulates transcriptional responses to diverse stress signals in bacteria.
Authors: Campbell, E.A. / Greenwell, R. / Anthony, J.R. / Wang, S. / Lim, L. / Das, K. / Sofia, H.J. / Donohue, T.J. / Darst, S.A.
History
DepositionMay 26, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: RpoE, ECF SigE
B: Anti-Sigma factor ChrR, transcriptional activator ChrR
C: RpoE, ECF SigE
D: Anti-Sigma factor ChrR, transcriptional activator ChrR
E: RpoE, ECF SigE
F: Anti-Sigma factor ChrR, transcriptional activator ChrR
G: RpoE, ECF SigE
H: Anti-Sigma factor ChrR, transcriptional activator ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,90714
Polymers172,4548
Non-polymers4546
Water6,864381
1
A: RpoE, ECF SigE
B: Anti-Sigma factor ChrR, transcriptional activator ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1793
Polymers43,1132
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
MethodPISA
2
C: RpoE, ECF SigE
D: Anti-Sigma factor ChrR, transcriptional activator ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1793
Polymers43,1132
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
MethodPISA
3
E: RpoE, ECF SigE
F: Anti-Sigma factor ChrR, transcriptional activator ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2754
Polymers43,1132
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
MethodPISA
4
G: RpoE, ECF SigE
H: Anti-Sigma factor ChrR, transcriptional activator ChrR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2754
Polymers43,1132
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.135, 46.452, 141.701
Angle α, β, γ (deg.)90.00, 91.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
RpoE, ECF SigE


Mass: 21309.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: rpoE / Plasmid: pET28a derivitive / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3IYV6
#2: Protein
Anti-Sigma factor ChrR, transcriptional activator ChrR


Mass: 21804.225 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: chrR / Plasmid: pET28a derivitive / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40685
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 0.2 M ammonium sulfate, 14-18% polyethylene glycol monomethylether 5000 (PEG5KMME), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97969 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2003
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97969 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 24975 / % possible obs: 75.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 9.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 2.14 / Num. unique all: 2887 / Rsym value: 0.079 / % possible all: 60.7

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→25 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.2865 1629 -random
Rwork0.25 ---
all0.2865 32734 --
obs0.2865 24975 75.2 %-
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9984 0 14 381 10379
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONrmsd bonds0.024922
X-RAY DIFFRACTIONrmsd angles2.2085

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