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- PDB-1iul: The structure of cell-free ID.343 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 1iul
TitleThe structure of cell-free 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 / MAD / Resolution: 2 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 1.3Dec 27, 2023Group: 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: hypothetical protein TT1466


Theoretical massNumber of molelcules
Total (without water)15,8891
Polymers15,8891
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.098, 64.890, 34.971
Angle α, β, γ (deg.)90.00, 106.48, 90.00
Int Tables number4
Space group name H-MP1211

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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) / Description: CELL-FREE PROTEIN SYNTHESIS SYSTEM / Plasmid: pET11b / References: UniProt: Q8GHJ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 35.66 %
Crystal growDetails: SODIUM ACETATE, AMMONIUM SULFATE, PEG MME 2000
Crystal grow
*PLUS
Temperature: 293 K / pH: 4.9 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.2 mg/mlprotein1drop
250 mMsodium acetate1reservoirpH4.9
3100 mMammonium sulfate1reservoir
415 %PEG2000 MME1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.9747, 0.9800, 0.9804, 0.9824
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 13, 2001 / Details: SI 111
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97471
20.981
30.98041
40.98241
ReflectionResolution: 2→13 Å / Num. obs: 8037 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.8
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.097 / % possible all: 91.5
Reflection
*PLUS
Lowest resolution: 13 Å / Num. measured all: 31394
Reflection shell
*PLUS
% possible obs: 91.5 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
X-PLOR3.851refinement
HKL-2000data reduction
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→13 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 428 5.3 %RANDOM
Rwork0.187 ---
obs0.199 8008 98.3 %-
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 0 121 1195
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d1
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.62
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.321.5
X-RAY DIFFRACTIONx_mcangle_it3.362
X-RAY DIFFRACTIONx_scbond_it3.692
X-RAY DIFFRACTIONx_scangle_it5.612.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 61 4.9 %
Rwork0.287 1178 -
obs--92.2 %
Refinement
*PLUS
Lowest resolution: 13 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.62

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