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- PDB-1iuk: The structure of native ID.343 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 1iuk
TitleThe structure of native ID.343 from Thermus thermophilus
Componentshypothetical protein TT1466
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyCoA binding domain / CoA binding domain / CoA-binding / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CoA-binding domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWada, T. / Shirouzu, M. / Park, S.-Y. / Tame, J.R. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of a conserved CoA-binding protein synthesized by a cell-free system.
Authors: Wada, T. / Shirouzu, M. / Terada, T. / Ishizuka, Y. / Matsuda, T. / Kigawa, T. / Kuramitsu, S. / Park, S.Y. / Tame, J.R. / Yokoyama, S.
History
DepositionMar 5, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Other
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: hypothetical protein TT1466


Theoretical massNumber of molelcules
Total (without water)15,8891
Polymers15,8891
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.908, 64.581, 67.858
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 hypothetical protein TT1466


Mass: 15889.452 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GHJ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.93 Å3/Da / Density % sol: 35.67 %
Crystal growTemperature: 293 K / Details: PEG400, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113.8 mg/mlprotein1drop
220 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 4, 2001
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 13461 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.122 / % possible all: 80.1
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 24119 / Num. measured all: 62895 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 80.1 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
X-PLOR3.851refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IUL

1iul


Resolution: 1.7→50 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 682 5.1 %RANDOM
Rwork0.22 ---
obs0.234 13445 95.3 %-
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1089 0 0 85 1174
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.911.5
X-RAY DIFFRACTIONx_mcangle_it2.842
X-RAY DIFFRACTIONx_scbond_it3.392
X-RAY DIFFRACTIONx_scangle_it5.142.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 100 4.8 %
Rwork0.33 1980 -
obs--90.8 %
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.81

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