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- PDB-3zxn: Moorella thermoacetica RsbS S58E -

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Basic information

Entry
Database: PDB / ID: 3zxn
TitleMoorella thermoacetica RsbS S58E
ComponentsANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN
KeywordsTRANSCRIPTION / GENE REGULATION
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
THIOCYANATE ION / Anti-sigma-factor antagonist (STAS) domain protein
Similarity search - Component
Biological speciesMOORELLA THERMOACETICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionAug 12, 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_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_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: ANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN
B: ANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3624
Polymers27,2462
Non-polymers1162
Water3,045169
1
A: ANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,6231
Polymers13,6231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7393
Polymers13,6231
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.940, 60.820, 88.910
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 / RSBS


Mass: 13623.000 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MOORELLA THERMOACETICA (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2RIF5
#2: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 58 TO GLU ENGINEERED RESIDUE IN CHAIN B, SER 58 TO GLU

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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: 2.66 Å3/Da / Density % sol: 53.81 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M HEPES PH7, 8% (W/V) PEG 8000, 0.1 M SODIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: May 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→49.94 Å / Num. obs: 21867 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 30.263 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

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

2vy9


Resolution: 1.9→29.144 Å / SU ML: 0.25 / σ(F): 1.25 / Phase error: 24.27 / Stereochemistry target values: ML
Details: RESIDUES 1-2, 23 AND 121 TO 123 ARE DISORDERED IN CHAIN A. RESIDUES 1-4 AND RESIDUES 119 TO 123 ARE DISORDERED IN CHAIN B.
RfactorNum. reflection% reflection
Rfree0.2404 2040 5 %
Rwork0.1919 --
obs0.1942 40692 98.67 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.257 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso mean: 38.582 Å2
Baniso -1Baniso -2Baniso -3
1-9.9862 Å20 Å20 Å2
2--2.0881 Å20 Å2
3----12.0742 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 6 169 1962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081854
X-RAY DIFFRACTIONf_angle_d1.0322521
X-RAY DIFFRACTIONf_dihedral_angle_d12.751698
X-RAY DIFFRACTIONf_chiral_restr0.067327
X-RAY DIFFRACTIONf_plane_restr0.004310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94420.30751580.2942561X-RAY DIFFRACTION99
1.9442-1.99280.29511410.26222590X-RAY DIFFRACTION99
1.9928-2.04670.3231210.23562623X-RAY DIFFRACTION99
2.0467-2.10690.2921430.22322563X-RAY DIFFRACTION99
2.1069-2.17490.26081450.22492631X-RAY DIFFRACTION99
2.1749-2.25260.25031300.20542596X-RAY DIFFRACTION99
2.2526-2.34280.26891250.18482590X-RAY DIFFRACTION99
2.3428-2.44930.26551120.18662609X-RAY DIFFRACTION100
2.4493-2.57840.28731340.19232605X-RAY DIFFRACTION99
2.5784-2.73980.28141450.19032596X-RAY DIFFRACTION99
2.7398-2.95120.24311390.20132588X-RAY DIFFRACTION99
2.9512-3.24780.2441380.18192589X-RAY DIFFRACTION99
3.2478-3.7170.2211570.17912591X-RAY DIFFRACTION100
3.717-4.67980.19131350.15792528X-RAY DIFFRACTION97
4.6798-29.14780.21681170.20082392X-RAY DIFFRACTION91

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