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- PDB-1vc1: Crystal structure of the TM1442 protein from Thermotoga maritima,... -

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Basic information

Entry
Database: PDB / ID: 1vc1
TitleCrystal structure of the TM1442 protein from Thermotoga maritima, a homolog of the Bacillus subtilis general stress response anti-anti-sigma factor RsbV
ComponentsPutative anti-sigma factor antagonist TM1442
KeywordsGENE REGULATION / ANTI-ANTI-SIGMA FACTOR
Function / homology
Function and homology information


anti-sigma factor antagonist activity
Similarity search - Function
Anti-sigma factor antagonist / STAS domain / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative anti-sigma factor antagonist TM_1442
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, J.Y. / Ahn, H.J. / Ha, K.S. / Suh, S.W.
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of the TM1442 protein from Thermotoga maritima, a homolog of the Bacillus subtilis general stress response anti-anti-sigma factor RsbV
Authors: Lee, J.Y. / Ahn, H.J. / Ha, K.S. / Suh, S.W.
History
DepositionMar 3, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative anti-sigma factor antagonist TM1442
B: Putative anti-sigma factor antagonist TM1442


Theoretical massNumber of molelcules
Total (without water)24,6342
Polymers24,6342
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-12 kcal/mol
Surface area10480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.544, 116.831, 31.392
Angle α, β, γ (deg.)90.00, 119.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative anti-sigma factor antagonist TM1442 / TM1442 protein / general stress response anti-anti-sigma factor


Mass: 12317.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1442 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1F5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 1.88 Å3/Da / Density % sol: 34.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM sodium acetate, 100mM magnesium chloride, 18%(v/v) polyethylene glycol 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 27, 1999
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 12862 / Num. obs: 12842 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16 Å2
Reflection shellResolution: 2→2.13 Å / % possible all: 94.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.92 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 807204.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1324 10.3 %RANDOM
Rwork0.205 ---
obs0.205 12842 96.4 %-
all-12862 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.886 Å2 / ksol: 0.35435 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-7.56 Å20 Å25.02 Å2
2---6.31 Å20 Å2
3----1.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 0 177 1903
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.233 210 10.1 %
Rwork0.264 1864 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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