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- PDB-3ut8: Structural view of a non Pfam singleton and crystal packing analysis -

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Basic information

Entry
Database: PDB / ID: 3ut8
TitleStructural view of a non Pfam singleton and crystal packing analysis
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / a non Pfam singleton / crystal packing analysis / helical fold / ytoplasm
Function / homologyDomain of unknown function DUF5071 / Domain of unknown function DUF5071 / Cthe_2751-like superfamily / Domain of unknown function (DUF5071) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / IODIDE ION / DUF5071 domain-containing protein
Function and homology information
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.168 Å
AuthorsCheng, C. / Shaw, N. / Zhang, X. / Zhang, M. / Ding, W. / Wang, B.C. / Liu, Z.J.
CitationJournal: Plos One / Year: 2012
Title: Structural view of a non pfam singleton and crystal packing analysis.
Authors: Cheng, C. / Shaw, N. / Zhang, X. / Zhang, M. / Ding, W. / Wang, B.C. / Liu, Z.J.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7717
Polymers31,1372
Non-polymers6355
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-19 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.105, 63.885, 96.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein / Cthe_2751


Mass: 15568.289 Da / Num. of mol.: 2 / Mutation: S124Y, T128Y, I129Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2751 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DJ21
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.49 Å3/Da / Density % sol: 50.61 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.541 Å
DetectorDate: Feb 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.168→30.58 Å / Num. obs: 16720 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.17→2.25 Å / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.168→27.148 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 838 5.01 %
Rwork0.2228 --
obs0.223 16720 97.74 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.088 Å2 / ksol: 0.307 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1639 Å2-0 Å2-0 Å2
2---1.1535 Å20 Å2
3----6.2399 Å2
Refinement stepCycle: LAST / Resolution: 2.168→27.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 5 126 2285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082224
X-RAY DIFFRACTIONf_angle_d1.0583031
X-RAY DIFFRACTIONf_dihedral_angle_d14.009845
X-RAY DIFFRACTIONf_chiral_restr0.075351
X-RAY DIFFRACTIONf_plane_restr0.012369
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1678-2.30350.21711360.2628248794
2.3035-2.48130.271480.25282651100
2.4813-2.73080.27291340.24752675100
2.7308-3.12540.25651620.24952677100
3.1254-3.93580.21821390.2171264898
3.9358-27.14990.18481190.1925274495

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