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- PDB-3ueb: Crystal structure of TON_0450 from Thermococcus onnurineus NA1 -

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Basic information

Entry
Database: PDB / ID: 3ueb
TitleCrystal structure of TON_0450 from Thermococcus onnurineus NA1
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / alpha and beta protein (a+b)
Function / homologyMTH677-like / Protein of unknown function DUF3194 / MTH677-like superfamily / Protein of unknown function (DUF3194) / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsKang, H.A. / Ku, B. / Doung, M. / Oh, B.H.
CitationJournal: To be Published
Title: Crystal structure of an Euryarchaeota-specific protein, TON_0450 from Thermococcus onnurineus NA1
Authors: Kang, H.A. / Ku, B. / Doung, M. / Oh, B.H.
History
DepositionOct 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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 uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
E: Putative uncharacterized protein
F: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)76,9596
Polymers76,9596
Non-polymers00
Water3,369187
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,6532
Polymers25,6532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-2 kcal/mol
Surface area10390 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,6532
Polymers25,6532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-0 kcal/mol
Surface area10650 Å2
MethodPISA
3
E: Putative uncharacterized protein
F: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,6532
Polymers25,6532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-5 kcal/mol
Surface area10730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.059, 108.059, 127.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Putative uncharacterized protein


Mass: 12826.491 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: TON_0450 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YTZ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1M Bis-Tris (PH5.3), 22% PEG 3350, 0.22M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.98→49.75 Å / Num. all: 99450 / Num. obs: 73191 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.98→49.75 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2527 --
Rwork0.2065 --
obs-52717 99.9 %
Solvent computationBsol: 35.0738 Å2
Displacement parametersBiso mean: 30.7135 Å2
Baniso -1Baniso -2Baniso -3
1-0.883 Å20 Å20 Å2
2--0.883 Å20 Å2
3----1.767 Å2
Refinement stepCycle: LAST / Resolution: 1.98→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 0 187 5166
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_d1.194
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_mcbond_it1.4471.5
X-RAY DIFFRACTIONc_scbond_it2.2952
X-RAY DIFFRACTIONc_mcangle_it2.3392
X-RAY DIFFRACTIONc_scangle_it3.462.5

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