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- PDB-1l7j: X-ray structure of galactose mutarotase from Lactococcus lactis (apo) -

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Basic information

Entry
Database: PDB / ID: 1l7j
TitleX-ray structure of galactose mutarotase from Lactococcus lactis (apo)
Componentsgalactose mutarotase
KeywordsISOMERASE / mutarotase / epimerase / galactose metabolism
Function / homology
Function and homology information


aldose 1-epimerase / aldose 1-epimerase activity / galactose catabolic process via UDP-galactose, Leloir pathway / glucose metabolic process / carbohydrate binding / cytoplasm
Similarity search - Function
Aldose 1-epimerase, bacterial / Aldose 1-epimerase / : / Aldose 1-/Glucose-6-phosphate 1-epimerase / Aldose 1-epimerase / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsHolden, H.M. / Thoden, J.B.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: High resolution X-ray structure of galactose mutarotase from Lactococcus lactis.
Authors: Thoden, J.B. / Holden, H.M.
History
DepositionMar 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: galactose mutarotase
B: galactose mutarotase


Theoretical massNumber of molelcules
Total (without water)77,2462
Polymers77,2462
Non-polymers00
Water13,872770
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.500, 76.100, 206.800
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 galactose mutarotase / aldose 1-epimerase


Mass: 38622.957 Da / Num. of mol.: 2 / Mutation: E2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: GALM / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9ZB17, aldose 1-epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG-5000-O-Methylether, MES, NaCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115-19 %PEG5000-OMe1reservoir
2100 mMMES1reservoirpH6.0
317.5 mg/mlenzyme1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 9, 2002 / Details: goebel mirrors
RadiationMonochromator: goebel optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 49650 / Num. obs: 49650 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.081 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 5683 / Rsym value: 0.18 / % possible all: 86.7
Reflection
*PLUS
Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 86.7 % / Num. unique obs: 5683 / Rmerge(I) obs: 0.18

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Processing

Software
NameClassification
SOLVEphasing
TNTrefinement
FRAMBOdata collection
SAINTdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 5090 -RANDOM
Rwork0.189 ---
all0.197 49650 --
obs0.197 49650 92.6 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5295 0 0 770 6065
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.45
X-RAY DIFFRACTIONt_bond_d0.014
Refinement
*PLUS
Num. reflection obs: 44968 / Rfactor all: 0.197 / Rfactor obs: 0.189 / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.5
X-RAY DIFFRACTIONt_planar_d0.006
X-RAY DIFFRACTIONt_plane_restr0.015

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