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- PDB-1ns2: Crystal structure of galactose mutarotase from Lactococcus lactis... -

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Basic information

Entry
Database: PDB / ID: 1ns2
TitleCrystal structure of galactose mutarotase from Lactococcus lactis mutant E304A complexed with galactose
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
beta-D-galactopyranose / NICKEL (II) ION / Aldose 1-epimerase
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsHolden, H.M. / Thoden, J.B.
CitationJournal: Protein Sci. / Year: 2003
Title: The Catalytic Mechanism of Galactose Mutarotase
Authors: Thoden, J.B. / Kim, J. / Raushel, F.M. / Holden, H.M.
History
DepositionJan 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GALACTOSE MUTAROTASE
B: GALACTOSE MUTAROTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5495
Polymers77,1302
Non-polymers4193
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-0 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.800, 76.400, 211.400
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: 38564.922 Da / Num. of mol.: 2 / Mutation: E304A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9ZB17, 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.: 2
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: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.23 Å3/Da / Density % sol: 44.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, methylether PEG-5000, NaCl, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115-19 %PEG5000 MME1reservoir
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: Mar 25, 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: 1.95→30 Å / Num. all: 50827 / Num. obs: 50827 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rsym value: 0.0702 / Net I/σ(I): 10.5
Reflection shellResolution: 1.95→2.04 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 5840 / Rsym value: 0.248 / % possible all: 86.8
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.0702

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Processing

Software
NameClassification
FRAMBOdata collection
SAINTdata reduction
TNTrefinement
SAINTdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1L7J

1l7j


Resolution: 1.95→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.229 5089 -RANDOM
Rwork0.163 ---
all0.166 50822 --
obs0.166 50822 94.1 %-
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5358 0 27 402 5787
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.33
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 45793
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.6
X-RAY DIFFRACTIONt_planar_d0.007
X-RAY DIFFRACTIONt_plane_restr0.012

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