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- PDB-3ut7: Structural view of a non Pfam singleton and crystal packing analysis -

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Basic information

Entry
Database: PDB / ID: 3ut7
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
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 / DUF5071 domain-containing protein
Function and homology information
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 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

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6642
Polymers15,5681
Non-polymers961
Water543
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3294
Polymers31,1372
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2150 Å2
ΔGint-38 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.509, 37.509, 169.749
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Putative uncharacterized protein / Cthe_2751


Mass: 15568.289 Da / Num. of mol.: 1 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 1.92 Å3/Da / Density % sol: 35.86 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorDate: Feb 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→42.44 Å / Num. obs: 2595 / % possible obs: 96.58 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 96.58

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→42.44 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23746 124 4.6 %RANDOM
Rwork0.21188 ---
obs0.21293 2562 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.797 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å20 Å2
2--2.9 Å20 Å2
3----5.8 Å2
Refinement stepCycle: LAST / Resolution: 3.01→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 0 5 3 1038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021065
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9831457
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3115128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.45125.12241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.4215189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.528152
X-RAY DIFFRACTIONr_chiral_restr0.1030.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021769
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.006→3.084 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 14 -
Rwork0.366 181 -
obs--97.5 %

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