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- PDB-1gd7: CRYSTAL STRUCTURE OF A BIFUNCTIONAL PROTEIN (CSAA) WITH EXPORT-RE... -

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Basic information

Entry
Database: PDB / ID: 1gd7
TitleCRYSTAL STRUCTURE OF A BIFUNCTIONAL PROTEIN (CSAA) WITH EXPORT-RELATED CHAPERONE AND TRNA-BINDING ACTIVITIES.
ComponentsCSAA PROTEIN
KeywordsRNA BINDING PROTEIN / OLIGONUCLEOTIDE-BINDING FOLD / FUNCTIONAL DIMER / HYDROPHOBIC CAVITY / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


Probable chaperone CsaA / : / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Export-related chaperone
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsShibata, T. / Inoue, Y. / Vassylyev, D.G. / Kawaguchi, S. / Yokoyama, S. / Muller, J. / Linde, D. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: EMBO J. / Year: 2001
Title: The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus.
Authors: Kawaguchi, S. / Muller, J. / Linde, D. / Kuramitsu, S. / Shibata, T. / Inoue, Y. / Vassylyev, D.G. / Yokoyama, S.
History
DepositionSep 22, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2001Provider: 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: CSAA PROTEIN
B: CSAA PROTEIN
C: CSAA PROTEIN
D: CSAA PROTEIN


Theoretical massNumber of molelcules
Total (without water)47,6604
Polymers47,6604
Non-polymers00
Water5,909328
1
A: CSAA PROTEIN
B: CSAA PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,8302
Polymers23,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-27 kcal/mol
Surface area10340 Å2
MethodPISA
2
C: CSAA PROTEIN
D: CSAA PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,8302
Polymers23,8302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-27 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.715, 55.715, 167.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological active assembly is a dimer of identical prtein subunits. There are two identical dimers in the asymmetric units with chain IDs: A-B and C-D.

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Components

#1: Protein
CSAA PROTEIN


Mass: 11914.991 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET15B-TTCSAA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AQH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: NaCl, Sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
23.8 M1reservoirNaCl
30.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 34223 / Num. obs: 33368 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.191 / Num. unique all: 3321 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 135225
Reflection shell
*PLUS
% possible obs: 94.5 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The merohedral twinning fraction of 0.047 was used during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1668 4.9988 %RANDOM
Rwork0.217 ---
all0.219 33368 --
obs0.219 33368 100 %-
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 0 328 3684
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_torsion_impr_deg0.9
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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