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- PDB-1lur: Crystal Structure of the GalM/aldose Epimerase Homologue from C. ... -

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Basic information

Entry
Database: PDB / ID: 1lur
TitleCrystal Structure of the GalM/aldose Epimerase Homologue from C. elegans, Northeast Structural Genomics Target WR66
Componentsaldose 1-epimerase
KeywordsISOMERASE / vitamin B12 / methyltransferase / structural genomics / structure-based function assignment / decarboxylase / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyBeta-galactosidase; Chain A, domain 5 - #10 / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich / Mainly Beta / :
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 1.85 Å
AuthorsKeller, J.P. / Xiao, R. / MacDonald, L. / Shen, J. / Acton, T. / Montelione, G. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the GalM/aldose Epimerase Homologue from C. elegans, Northeast Structural Genomics Target WR66
Authors: Keller, J.P. / Xiao, R. / MacDonald, L. / Shen, J. / Acton, T. / Montelione, G. / Hunt, J.F.
History
DepositionMay 23, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aldose 1-epimerase
B: aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1014
Polymers75,9092
Non-polymers1922
Water7,170398
1
A: aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0512
Polymers37,9551
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0512
Polymers37,9551
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.808, 91.007, 83.701
Angle α, β, γ (deg.)90.00, 100.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein aldose 1-epimerase


Mass: 37954.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NESG WR66 / Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pET14c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q966D4, aldose 1-epimerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: PEG 600, Lithium Sulfate, TrisCl, PEG 4000, Glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 15, 2001 / Details: Yale Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. all: 141930 / Num. obs: 131853 / % possible obs: 92.9 % / Observed criterion σ(F): -5 / Observed criterion σ(I): -5 / Redundancy: 3.36 % / Rsym value: 0.05 / Net I/σ(I): 24.35

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.85→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3006 -5%
Rwork0.224 ---
all0.224 63867 --
obs0.224 60770 95.2 %-
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5096 0 10 398 5504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_angle_deg1.509

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