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- PDB-3s4c: Lactose phosphorylase in complex with sulfate -

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Basic information

Entry
Database: PDB / ID: 3s4c
TitleLactose phosphorylase in complex with 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
1,4-DIETHYLENE DIOXIDE / Cellobiose phosphorylase
Similarity search - Component
Biological speciesCellulomonas uda (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)91,6843
Polymers91,5001
Non-polymers1842
Water8,899494
1
A: Lactose Phosphorylase
hetero molecules

A: Lactose Phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,3686
Polymers183,0002
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7420 Å2
ΔGint-47 kcal/mol
Surface area47950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.450, 93.210, 106.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-824-

DIO

21A-1176-

HOH

31A-1189-

HOH

41A-1291-

HOH

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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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulfate, 0.1M Mes monohydrate pH6.5, 10% 1,4-dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2009
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→19.82 Å / Num. all: 33898 / Num. obs: 33519 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.47 Å2
Reflection shellResolution: 2.4→2.46 Å / % possible all: 89.2

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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: 2.4→19.82 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.33 / σ(F): 1.99 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 335 1 %random
Rwork0.1823 ---
obs0.1826 33444 98.9 %-
all-33444 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.982 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso max: 67.84 Å2 / Biso mean: 21.4235 Å2 / Biso min: 9.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.8443 Å2-0 Å20 Å2
2---2.9495 Å2-0 Å2
3---2.1053 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 11 494 6904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076592
X-RAY DIFFRACTIONf_angle_d1.138993
X-RAY DIFFRACTIONf_chiral_restr0.062955
X-RAY DIFFRACTIONf_plane_restr0.0051192
X-RAY DIFFRACTIONf_dihedral_angle_d15.5342313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-3.02220.27541640.22162101637498
3.0222-19.820.18221710.16311689917070100

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