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- PDB-1wol: Crystal Structure of ST0689, an archaeal HEPN homologue -

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Basic information

Entry
Database: PDB / ID: 1wol
TitleCrystal Structure of ST0689, an archaeal HEPN homologue
Components122aa long conserved hypothetical protein
KeywordsUNKNOWN FUNCTION / ALPHA HELIX / LOOP
Function / homology
Function and homology information


HEPN domain profile. / Higher Eukarytoes and Prokaryotes Nucleotide-binding domain / HEPN domain / HEPN domain / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
TERTIARY-BUTYL ALCOHOL / HEPN domain-containing protein
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.62 Å
AuthorsArakawa, T. / Akutsu, J. / Yohda, M.
CitationJournal: To be Published
Title: Crystal Structure Analysis of ST0689, an archaeal HEPN protein
Authors: Arakawa, T. / Akutsu, J. / Yohda, M.
History
DepositionAug 20, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 122aa long conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3313
Polymers14,1831
Non-polymers1482
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.553, 62.553, 64.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly seems to be a monomer

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Components

#1: Protein 122aa long conserved hypothetical protein / ST0689


Mass: 14183.036 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: str. 7 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): B834, BL21(DE3) / References: UniProt: Q974G3
#2: Chemical ChemComp-TBU / TERTIARY-BUTYL ALCOHOL / 2-METHYL-2-PROPANOL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: tert-butanol, citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9765, 0.97894, 0.97924
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2004
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97651
20.978941
30.979241
ReflectionResolution: 1.62→50 Å / Biso Wilson estimate: 22.2 Å2
Reflection shellResolution: 1.62→1.68 Å / Rsym value: 0.177 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.62→41.35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 335259.04 / 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
Rfree0.222 3400 9.7 %RANDOM
Rwork0.187 ---
obs0.187 35163 98.6 %-
all-35646 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.7591 Å2 / ksol: 0.378148 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20.62 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.62→41.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 10 84 1091
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.041
X-RAY DIFFRACTIONc_angle_deg3.6
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d3.02
X-RAY DIFFRACTIONc_mcbond_it1.881.5
X-RAY DIFFRACTIONc_mcangle_it3.012
X-RAY DIFFRACTIONc_scbond_it2.782
X-RAY DIFFRACTIONc_scangle_it42.5
LS refinement shellResolution: 1.62→1.72 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 555 9.7 %
Rwork0.209 5176 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3T-BUTANOL.PARAMT-BUTANOL.TOP

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