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

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Basic information

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


Globin-like - #130 / : / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / Globin-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Anti-sigma-factor antagonist (STAS) domain protein
Similarity search - Component
Biological speciesMOORELLA THERMOACETICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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

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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


Theoretical massNumber of molelcules
Total (without water)16,8151
Polymers16,8151
Non-polymers00
Water905
1
A: ANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN

A: ANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,6292
Polymers33,6292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area2340 Å2
ΔGint-16.8 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.410, 56.410, 148.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

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Components

#1: Protein ANTI-SIGMA-FACTOR ANTAGONIST (STAS) DOMAIN PROTEIN / MTR


Mass: 16814.637 Da / Num. of mol.: 1 / Fragment: NON-HEME GLOBIN SIGNALLING DOMAIN, RESIDUES 1-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MOORELLA THERMOACETICA (bacteria) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / References: UniProt: Q2RIF4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.83 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 5.5
Details: 1.0 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS PROPANE, PH 5.5, 1% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9716
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 18, 2009
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9716 Å / Relative weight: 1
ReflectionResolution: 2.7→52.72 Å / Num. obs: 12435 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 52.3 % / Biso Wilson estimate: 56.69 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 49.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 55.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 16.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.7→52.725 Å / SU ML: 0.43 / σ(F): 0 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 591 4.8 %
Rwork0.214 --
obs0.2167 12435 99 %
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.141 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 68.8 Å2
Baniso -1Baniso -2Baniso -3
1--15.495 Å20 Å20 Å2
2---15.495 Å20 Å2
3---30.9901 Å2
Refinement stepCycle: LAST / Resolution: 2.7→52.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 0 5 1118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121219
X-RAY DIFFRACTIONf_angle_d0.7341514
X-RAY DIFFRACTIONf_dihedral_angle_d16.222423
X-RAY DIFFRACTIONf_chiral_restr0.057180
X-RAY DIFFRACTIONf_plane_restr0.003192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.97170.38351380.28162917X-RAY DIFFRACTION97
2.9717-3.40170.27321580.24532944X-RAY DIFFRACTION99
3.4017-4.28550.2891520.19622982X-RAY DIFFRACTION100
4.2855-52.7350.23841430.23001X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.40070.1221-1.44060.0124-0.12641.4885-0.2769-0.2827-0.37350.10080.0752-0.15970.42820.3085-1.66340.34640.0364-0.11450.20750.0240.263814.517917.858678.489
20.3745-0.1966-0.40850.10270.21350.446-0.21640.02290.35080.1662-0.0143-0.3203-0.52170.2992-0.25990.5441-0.018-0.27530.1950.0190.52739.433428.054280.7389
30.13930.1831-0.0640.88470.41690.4265-0.14610.1619-0.0798-0.34120.1146-0.062-0.0611-0.06310.88250.6012-0.0202-0.24760.2171-0.08970.53953.726311.404770.2298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 8:75)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 76:100)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 101:146)

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