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- PDB-1geq: Entropic stabilization of the tryptophan synthase A-subunit from ... -

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Basic information

Entry
Database: PDB / ID: 1geq
TitleEntropic stabilization of the tryptophan synthase A-subunit from a hyperthermophile, pyrococcus furiosus: X-ray analysis and calorimetry
ComponentsTRYPTOPHAN SYNTHASE ALPHA-SUBUNIT
KeywordsLYASE / Tryptophan Synthase alpha-Subunit / Hyperthermophile / Pyrococcus furiosus / X-ray Analysis / Stability / Calorimetry
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / cytosol
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsYutani, K. / Yamagata, Y.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry.
Authors: Yamagata, Y. / Ogasahara, K. / Hioki, Y. / Lee, S.J. / Nakagawa, A. / Nakamura, H. / Ishida, M. / Kuramitsu, S. / Yutani, K.
History
DepositionNov 21, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 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: TRYPTOPHAN SYNTHASE ALPHA-SUBUNIT
B: TRYPTOPHAN SYNTHASE ALPHA-SUBUNIT


Theoretical massNumber of molelcules
Total (without water)55,0722
Polymers55,0722
Non-polymers00
Water7,584421
1
A: TRYPTOPHAN SYNTHASE ALPHA-SUBUNIT


Theoretical massNumber of molelcules
Total (without water)27,5361
Polymers27,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRYPTOPHAN SYNTHASE ALPHA-SUBUNIT


Theoretical massNumber of molelcules
Total (without water)27,5361
Polymers27,5361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.013, 78.997, 170.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-372-

HOH

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Components

#1: Protein TRYPTOPHAN SYNTHASE ALPHA-SUBUNIT


Mass: 27535.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PA1974 / Production host: Escherichia coli (E. coli) / Strain (production host): E.COLI-109 / References: UniProt: Q8U094, tryptophan synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES-NaOH, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal
*PLUS
Density % sol: 53.4 %
Crystal grow
*PLUS
Temperature: 10 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MMes-NaOH1reservoir
212 %PEG200001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Apr 23, 1999
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 31934 / Num. obs: 31934 / % possible obs: 94.2 % / Redundancy: 2.84 % / Rmerge(I) obs: 0.0353 / Net I/σ(I): 30.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 7.3 / Num. unique all: 1557 / % possible all: 93.9
Reflection
*PLUS
Num. measured all: 90544 / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
% possible obs: 93.9 %

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2→40 Å / Isotropic thermal model: Isotropic / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1510 -RANDOM
Rwork0.198 ---
all-31426 --
obs-30701 90.8 %-
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 0 421 4238
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shellResolution: 2→2.02 Å
RfactorNum. reflection
Rfree0.2707 57
Rwork0.238 -
obs-896

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