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- PDB-1gn0: Escherichia coli GlpE sulfurtransferase soaked with KCN -

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Basic information

Entry
Database: PDB / ID: 1gn0
TitleEscherichia coli GlpE sulfurtransferase soaked with KCN
ComponentsTHIOSULFATE SULFURTRANSFERASE GLPE
KeywordsTRANSFERASE / RHODANESE / SULFURTRANSFERASE / GLYCEROL METABOLISM
Function / homology
Function and homology information


sulfur utilization / thiosulfate sulfurtransferase / glycerol metabolic process / thiosulfate sulfurtransferase activity / cytoplasm
Similarity search - Function
Thiosulfate sulfurtransferase, bacterial / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiosulfate sulfurtransferase GlpE
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.8 Å
AuthorsSpallarossa, A. / Donahue, J.T. / Larson, T.J. / Bolognesi, M. / Bordo, D.
CitationJournal: Structure / Year: 2001
Title: Escherichia Coli Glpe is a Prototype Sulfurtransferase for the Single-Domain Rhodanese Homology Superfamily
Authors: Spallarossa, A. / Donahue, J.T. / Larson, T.J. / Bolognesi, M. / Bordo, D.
History
DepositionOct 1, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2001Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THIOSULFATE SULFURTRANSFERASE GLPE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1773
Polymers12,0921
Non-polymers852
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.796, 53.796, 30.346
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein THIOSULFATE SULFURTRANSFERASE GLPE / GLPE PROTEIN


Mass: 12092.421 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A6V5, thiosulfate sulfurtransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18 mg/mlprotein1drop
250 mMTris-HCl1droppH7.0
33 mMEDTA1drop
4100 mM1dropNaCl
510 %(v/v)glycerol1drop
60.1 M1reservoirCaCl2
70.1 Msodium acetate1reservoirpH4.6
820 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→18 Å / Num. obs: 9094 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 23
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 2.5 / % possible all: 85
Reflection
*PLUS
Lowest resolution: 18 Å / % possible obs: 95.7 % / Num. measured all: 64419
Reflection shell
*PLUS
% possible obs: 84.7 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.8→20 Å / SU B: 3.52667 / SU ML: 0.11246 / Cross valid method: THROUGHOUT / ESU R: 0.1474 / ESU R Free: 0.15556 / Details: NONE
RfactorNum. reflection% reflectionSelection details
Rfree0.24822 414 4.8 %RANDOM
Rwork0.17348 ---
obs0.17715 8281 96 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms849 0 5 88 942
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.177 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4

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