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- PDB-3rsy: Cellobiose phosphorylase from Cellulomonas uda in complex with su... -

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Basic information

Entry
Database: PDB / ID: 3rsy
TitleCellobiose phosphorylase from Cellulomonas uda in complex with sulfate and glycerol
ComponentsCellobiose phosphorylase
KeywordsTRANSFERASE / GH94 / alpha barrel / cellobiose 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
Cellobiose phosphorylase
Similarity search - Component
Biological speciesCellulomonas uda (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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 2, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Cellobiose phosphorylase
B: Cellobiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,81510
Polymers183,0622
Non-polymers7538
Water27,4191522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-81 kcal/mol
Surface area49020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.100, 103.780, 99.150
Angle α, β, γ (deg.)90.000, 96.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cellobiose phosphorylase /


Mass: 91530.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1522 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0015 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2007
RadiationMonochromator: Fixed-exit LN2 cooled Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 1.81→19.976 Å / Num. all: 157280 / Num. obs: 148787 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.41 Å2
Reflection shellResolution: 1.81→1.86 Å / % possible all: 87.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→19.976 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8509 / SU ML: 0.25 / σ(F): 2 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 7440 5 %RANDOM
Rwork0.202 ---
obs0.2038 148787 94.6 %-
all-148787 --
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.438 Å2 / ksol: 0.445 e/Å3
Displacement parametersBiso max: 79.04 Å2 / Biso mean: 20.4404 Å2 / Biso min: 3.48 Å2
Baniso -1Baniso -2Baniso -3
1--4.7167 Å2-0 Å21.623 Å2
2---1.6697 Å2-0 Å2
3---6.3864 Å2
Refinement stepCycle: LAST / Resolution: 1.81→19.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12852 0 44 1522 14418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01613414
X-RAY DIFFRACTIONf_angle_d1.53718339
X-RAY DIFFRACTIONf_chiral_restr0.0891931
X-RAY DIFFRACTIONf_plane_restr0.0092447
X-RAY DIFFRACTIONf_dihedral_angle_d14.5964757
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.81-1.87490.34016980.2865132701396889
1.8749-1.94990.30727360.262139851472194
1.9499-2.03860.29167400.236140601480095
2.0386-2.1460.27037470.2139141871493495
2.146-2.28020.24747500.2004142541500496
2.2802-2.4560.24317510.1934142631501496
2.456-2.70260.23917590.1916144191517896
2.7026-3.09250.21997570.1826143911514896
3.0925-3.89150.20967500.1765142381498895
3.8915-19.97690.20347520.1956142801503294

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