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- PDB-3ztb: The bacterial stressosome: a modular system that has been adapted... -

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Basic information

Entry
Database: PDB / ID: 3ztb
TitleThe bacterial stressosome: a modular system that has been adapted to control secondary messenger signaling
ComponentsANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN
KeywordsSIGNALING / STRESSOSOME / SIGNAL TRANSDUCTION / PHOSPHORYLATION / PROTEIN-PROTEIN INTERACTION / TYPE 2C PHOSPHATASES / RSBS
Function / homology
Function and homology information


: / STAS domain / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Anti-sigma-factor antagonist (STAS) domain protein
Similarity search - Component
Biological speciesMOORELLA THERMOACETICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsQuin, M.B. / Berrisford, J.M. / Newman, J.A. / Basle, A. / Lewis, R.J. / Marles-Wright, J.
CitationJournal: Structure / Year: 2012
Title: The Bacterial Stressosome: A Modular System that Has Been Adapted to Control Secondary Messenger Signaling.
Authors: Quin, M.B. / Berrisford, J.M. / Newman, J.A. / Basle, A. / Lewis, R.J. / Marles-Wright, J.
History
DepositionJul 6, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn / struct_site
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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN
B: ANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5764
Polymers27,3222
Non-polymers2542
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-2.2 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.537, 60.976, 88.954
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 ANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN / MTS


Mass: 13660.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED SER58 / Source: (gene. exp.) MOORELLA THERMOACETICA (bacteria) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q2RIF5
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.77 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6.5
Details: 1 UL PROTEIN AND 1 UL CRYSTALLANT, 1 ML WELL, 20 % PEG 3350, 0.2 M NAI, 0.1 M BIS-TRIS, PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2010
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.8→61 Å / Num. obs: 7170 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 42.86 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.1
Reflection shellResolution: 2.8→3.52 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VY9

2vy9


Resolution: 2.8→19.815 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2732 330 4.7 %
Rwork0.2105 --
obs0.2137 6990 97.87 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.584 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.0777 Å20 Å20 Å2
2--4.9255 Å20 Å2
3----11.0031 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 2 10 1774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041783
X-RAY DIFFRACTIONf_angle_d0.9082421
X-RAY DIFFRACTIONf_dihedral_angle_d18.148660
X-RAY DIFFRACTIONf_chiral_restr0.05311
X-RAY DIFFRACTIONf_plane_restr0.003295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.52460.33031680.2563181X-RAY DIFFRACTION96
3.5246-19.81510.24011620.18953479X-RAY DIFFRACTION100

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