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- PDB-1so0: Crystal structure of human galactose mutarotase complexed with ga... -

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Basic information

Entry
Database: PDB / ID: 1so0
TitleCrystal structure of human galactose mutarotase complexed with galactose
Componentsaldose 1-epimerase
KeywordsISOMERASE / mutartoase / epimerase / galactosemia
Function / homology
Function and homology information


aldose 1-epimerase / aldose 1-epimerase activity / galactose catabolic process via UDP-galactose / galactose metabolic process / glucose metabolic process / carbohydrate binding / carbohydrate metabolic process / extracellular exosome / cytoplasm
Similarity search - Function
Aldose 1-epimerase, conserved site / Aldose 1-epimerase putative active site. / : / 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 ...Aldose 1-epimerase, conserved site / Aldose 1-epimerase putative active site. / : / 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
beta-D-galactopyranose / Galactose mutarotase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsThoden, J.B. / Timson, D.J. / Reece, R.J. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Molecular structure of human galactose mutarotase
Authors: Thoden, J.B. / Timson, D.J. / Reece, R.J. / Holden, H.M.
History
DepositionMar 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)152,7438
Polymers152,0224
Non-polymers7214
Water7,314406
1
A: aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1862
Polymers38,0061
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1862
Polymers38,0061
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1862
Polymers38,0061
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: aldose 1-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1862
Polymers38,0061
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.000, 68.700, 98.900
Angle α, β, γ (deg.)107.70, 98.40, 102.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
aldose 1-epimerase / galactose mutarotase


Mass: 38005.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALM / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q96C23, aldose 1-epimerase
#2: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.47 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 275 K / Method: batch / pH: 6
Details: PEG 8000, sodium chloride, lithium chloride, galactose, MES, pH 6.0, batch, temperature 275K

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Feb 10, 2004 / Details: super long mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 61156 / Num. obs: 61156 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rsym value: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 5979 / Rsym value: 0.264 / % possible all: 77.5

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Processing

Software
NameClassification
FRAMBOdata collection
SAINTdata reduction
AMoREphasing
TNTrefinement
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1snz

1snz


Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 6116 -random
Rwork0.167 ---
all0.169 61156 --
obs0.169 61156 94.7 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10746 0 48 406 11200
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg2.4

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