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- PDB-3rrs: Crystal structure analysis of cellobiose phosphorylase from Cellu... -

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Basic information

Entry
Database: PDB / ID: 3rrs
TitleCrystal structure analysis of cellobiose phosphorylase from Cellulomonas uda
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 ...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: 1.7 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
DepositionApr 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Cellobiose phosphorylase
B: Cellobiose phosphorylase


Theoretical massNumber of molelcules
Total (without water)183,0622
Polymers183,0622
Non-polymers00
Water40,1012226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-13 kcal/mol
Surface area49500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.690, 103.800, 98.500
Angle α, β, γ (deg.)90.000, 96.510, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2226 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4M Na Formate, 20mM alpha-glucose-!-phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.98345 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2008
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98345 Å / Relative weight: 1
ReflectionResolution: 1.7→19.751 Å / Num. all: 187812 / Num. obs: 181274 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.01 Å2
Reflection shellResolution: 1.7→1.74 Å / % possible all: 95.5

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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: 1.7→19.751 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.8722 / SU ML: 0.18 / σ(F): 1.99 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 1812 1 %RANDOM
Rwork0.1853 ---
obs0.1855 181260 96.59 %-
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.83 Å2 / ksol: 0.477 e/Å3
Displacement parametersBiso max: 78.46 Å2 / Biso mean: 16.5992 Å2 / Biso min: 2.14 Å2
Baniso -1Baniso -2Baniso -3
1--3.4803 Å20 Å2-0.7311 Å2
2---0.8735 Å2-0 Å2
3---4.3539 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12901 0 0 2226 15127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01613549
X-RAY DIFFRACTIONf_angle_d1.51618550
X-RAY DIFFRACTIONf_chiral_restr0.091967
X-RAY DIFFRACTIONf_plane_restr0.0082477
X-RAY DIFFRACTIONf_dihedral_angle_d13.6184886
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 (%)
1.7-1.76070.32121770.254176871786496
1.7607-1.83120.26141800.2317177341791496
1.8312-1.91450.24361800.2121178561803696
1.9145-2.01530.23091810.1953179741815597
2.0153-2.14140.19591810.1823178821806396
2.1414-2.30650.22921810.1758179151809697
2.3065-2.53820.22091830.1753181261830998
2.5382-2.90450.18721840.1753181901837498
2.9045-3.65560.1921830.1672181541833797
3.6556-19.7510.17321820.1807179301811295

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