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- PDB-3qtp: Crystal Structure Analysis of Entamoeba histolytica Enolase -

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Basic information

Entry
Database: PDB / ID: 3qtp
TitleCrystal Structure Analysis of Entamoeba histolytica Enolase
ComponentsEnolase 1
KeywordsLYASE / Glycolysis / Enolase
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / glycolytic process / magnesium ion binding
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-PHOSPHOGLYCERIC ACID / Enolase 1
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSchulz, E.C. / Ficner, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure analysis of Entamoeba histolytica enolase.
Authors: Schulz, E.C. / Tietzel, M. / Tovy, A. / Ankri, S. / Ficner, R.
History
DepositionFeb 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enolase 1
B: Enolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,59012
Polymers95,5932
Non-polymers99710
Water20,1411118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-102 kcal/mol
Surface area29610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.420, 92.620, 160.580
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 Enolase 1 / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase


Mass: 47796.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: ENL-1 / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51555, phosphopyruvate hydratase
#2: Chemical ChemComp-2PG / 2-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1118 / 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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1M bis-Tris, 25% PEG 3350 (v/v), 0.2M (NH4)2SO4, pH 5,5, vapor diffusion, temperature 298K
PH range: 5,5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.981 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 75593 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.23 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-20.43.38192.9
2-2.50.1886.97199.7
2.5-2.60.11410.78199.9
2.6-2.80.09612.59199.9
2.8-30.07416.03199.9
3-50.04424.84199.8
5-80.03528.83199.9
8-100.02339.37199.8
10-200.02139.52199.4
20-500.02134.32185.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
PHENIX1.6.4_486refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.31 Å / Occupancy max: 1 / Occupancy min: 0.07 / SU ML: 0.19 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.202 3779 5 %
Rwork0.153 --
obs0.155 75582 99.5 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.16 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 15.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.6539 Å20 Å2-0 Å2
2--0.2556 Å2-0 Å2
3----0.9095 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 54 1118 7820

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