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- PDB-3zpj: Crystal structure of Ton1535 from Thermococcus onnurineus NA1 -

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Basic information

Entry
Database: PDB / ID: 3zpj
TitleCrystal structure of Ton1535 from Thermococcus onnurineus NA1
ComponentsTON_1535
KeywordsUNKNOWN FUNCTION / SOLENOID PROTEIN / HYPOTHETICAL PROTEIN / RIGHT-HANDED COILED COIL / LEFT-HANDED HELIX TURN
Function / homologyTetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / TRP-repeat-containing protein
Function and homology information
Biological speciesTHERMOCOCCUS ONNURINEUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.304 Å
AuthorsJeong, J.H. / kim, Y.G.
CitationJournal: Proteins / Year: 2014
Title: Structure of the Hypothetical Protein Ton1535 from Thermococcus Onnurineus Na1 Reveals Unique Structural Properties by a Left-Handed Helical Turn in Normal Alpha-Solenoid Protein.
Authors: Jeong, J. / Kim, Y. / Rojvirija, C. / Cha, H.J. / Kim, Y. / Ha, S.C.
History
DepositionFeb 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TON_1535


Theoretical massNumber of molelcules
Total (without water)40,9541
Polymers40,9541
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.954, 117.954, 208.232
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein TON_1535


Mass: 40954.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS ONNURINEUS (archaea) / Strain: NA1 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834(DE3) RIL / References: UniProt: B6YTT4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 1.71 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M BIS-TRIS PROPANE (PH7.0), 1.2 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2011 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 24870 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 41.33 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 45.5
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 9.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.304→29.911 Å / SU ML: 0.29 / σ(F): 1.29 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1268 5.1 %
Rwork0.1943 --
obs0.1969 24870 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.5 Å2
Refinement stepCycle: LAST / Resolution: 2.304→29.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 0 8 2858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082898
X-RAY DIFFRACTIONf_angle_d1.1393911
X-RAY DIFFRACTIONf_dihedral_angle_d14.4191106
X-RAY DIFFRACTIONf_chiral_restr0.076450
X-RAY DIFFRACTIONf_plane_restr0.005498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3036-2.39580.30711370.26352572X-RAY DIFFRACTION100
2.3958-2.50480.31571330.25192623X-RAY DIFFRACTION99
2.5048-2.63680.2841310.23712584X-RAY DIFFRACTION100
2.6368-2.80190.30251500.22562596X-RAY DIFFRACTION100
2.8019-3.0180.2771440.2322595X-RAY DIFFRACTION100
3.018-3.32140.28581470.22262597X-RAY DIFFRACTION100
3.3214-3.80110.24021520.19032622X-RAY DIFFRACTION100
3.8011-4.78590.19341300.16072659X-RAY DIFFRACTION100
4.7859-29.91330.21381440.16412754X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.2702 Å / Origin y: 12.7587 Å / Origin z: 41.1984 Å
111213212223313233
T0.2255 Å2-0.0215 Å2-0.0219 Å2-0.2541 Å20.0347 Å2--0.3032 Å2
L1.7618 °2-0.4047 °2-0.7312 °2-1.7948 °20.6512 °2--1.6618 °2
S0.0016 Å °0.1655 Å °0.2353 Å °-0.1739 Å °-0.019 Å °-0.2529 Å °-0.055 Å °-0.0095 Å °0.021 Å °
Refinement TLS groupSelection details: ALL

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