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- PDB-3s4d: Lactose phosphorylase in a ternary complex with cellobiose and sulfate -

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Basic information

Entry
Database: PDB / ID: 3s4d
TitleLactose phosphorylase in a ternary complex with cellobiose and sulfate
ComponentsLactose Phosphorylase
KeywordsTRANSFERASE / GH94 / alpha barrel / lactose phosphorylase / disaccharide phosphorylase
Function / homology
Function and homology information


cellobiose phosphorylase / cellobiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
mpn423 like domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Cellobiose phosphorylase, N-terminal / Putative carbohydrate binding domain / Putative carbohydrate binding domain / cAMP-dependent Protein Kinase, Chain A / Glycosyl hydrolase 94 / Glycosyltransferase family 36 ...mpn423 like domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Cellobiose phosphorylase, N-terminal / Putative carbohydrate binding domain / Putative carbohydrate binding domain / cAMP-dependent Protein Kinase, Chain A / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Glycosyltransferase - #10 / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-cellobiose / Cellobiose phosphorylase
Similarity search - Component
Biological speciesCellulomonas uda (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsVan Hoorebeke, A. / Stout, J. / Soetaert, W. / Van Beeumen, J. / Desmet, T. / Savvides, S.
CitationJournal: To be Published
Title: Cellobiose phosphorylase: reconstructing the structural itinerary along the catalytic pathway
Authors: Van Hoorebeke, A. / Stout, J. / Soetaert, W. / Van Beeumen, J. / Desmet, T. / Savvides, S.
History
DepositionMay 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: Lactose Phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9383
Polymers91,5001
Non-polymers4382
Water724
1
A: Lactose Phosphorylase
hetero molecules

A: Lactose Phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,8776
Polymers183,0002
Non-polymers8774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9020 Å2
ΔGint-41 kcal/mol
Surface area47940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.710, 92.880, 104.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lactose Phosphorylase


Mass: 91499.992 Da / Num. of mol.: 1 / Mutation: T508I, N667A
Source method: isolated from a genetically manipulated source
Details: Lactose phosphorylase is a T508I/N667A mutant created through directed evolution from cellobiose phosphorylase from Cellulomoas uda.
Source: (gene. exp.) Cellulomonas uda (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7WTR6, cellobiose phosphorylase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.5M ammonium sulate, 1.0M lithium sulfate, 0.1M tri-sodium citrate dehydrate pH5.6 soaked with 0.5M ammonium sulate, 1.0M lithium sulfate, 0.1M tri-sodium citrate dehydrate pH5.6, 50mM ...Details: 0.5M ammonium sulate, 1.0M lithium sulfate, 0.1M tri-sodium citrate dehydrate pH5.6 soaked with 0.5M ammonium sulate, 1.0M lithium sulfate, 0.1M tri-sodium citrate dehydrate pH5.6, 50mM cellobiose, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2009
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→38.54 Å / Num. all: 12961 / Num. obs: 12806 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.3→3.39 Å / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→38.54 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.52 / σ(F): 1.99 / Phase error: 32.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3402 127 99 %random
Rwork0.2962 ---
obs0.2966 12779 98.9 %-
all-12779 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.972 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 65.05 Å2 / Biso mean: 27.8964 Å2 / Biso min: 13.78 Å2
Baniso -1Baniso -2Baniso -3
1--3.2013 Å2-0 Å20 Å2
2---12.9531 Å2-0 Å2
3---16.1544 Å2
Refinement stepCycle: LAST / Resolution: 3.3→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 0 28 4 6328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096496
X-RAY DIFFRACTIONf_angle_d1.3768886
X-RAY DIFFRACTIONf_chiral_restr0.09963
X-RAY DIFFRACTIONf_plane_restr0.0071175
X-RAY DIFFRACTIONf_dihedral_angle_d21.5142268

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