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- PDB-3s4b: Cellobiose phosphorylase from Cellulomonas uda in complex with glucose -

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Basic information

Entry
Database: PDB / ID: 3s4b
TitleCellobiose phosphorylase from Cellulomonas uda in complex with glucose
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 / Cellobiose phosphorylase, N-terminal / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Glycoside hydrolase, family 65, N-terminal domain / Putative carbohydrate binding domain / Putative carbohydrate binding domain / cAMP-dependent Protein Kinase, Chain A / : / Glycosyl hydrolase 94 ...mpn423 like domain / Cellobiose phosphorylase, N-terminal / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Glycoside hydrolase, family 65, N-terminal domain / Putative carbohydrate binding domain / Putative carbohydrate binding domain / cAMP-dependent Protein Kinase, Chain A / : / Glycosyl hydrolase 94 / Glycosyl hydrolase 94, supersandwich domain / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 94 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
alpha-D-glucopyranose / 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 1.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)183,7836
Polymers183,0622
Non-polymers7214
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint3 kcal/mol
Surface area48040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.417, 102.740, 98.305
Angle α, β, γ (deg.)90.000, 96.440, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALAchain B and (resseq 1:207 or resseq 209:328 or resseq...BB1 - 2071 - 207
12GLYGLYASPASPchain B and (resseq 1:207 or resseq 209:328 or resseq...BB209 - 328209 - 328
13LYSLYSMETMETchain B and (resseq 1:207 or resseq 209:328 or resseq...BB330 - 555330 - 555
14ASPASPLEULEUchain B and (resseq 1:207 or resseq 209:328 or resseq...BB557 - 822557 - 822
21METMETALAALAchain A and (resseq 1:207 or resseq 209:328 or resseq...AA1 - 2071 - 207
22GLYGLYASPASPchain A and (resseq 1:207 or resseq 209:328 or resseq...AA209 - 328209 - 328
23LYSLYSMETMETchain A and (resseq 1:207 or resseq 209:328 or resseq...AA330 - 555330 - 555
24ASPASPLEULEUchain A and (resseq 1:207 or resseq 209:328 or resseq...AA557 - 822557 - 822

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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: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 3.4M sodium formate, 0.1M sodium acetate trihydrate, pH4.6, 20mM alpha-D-glucose 1-phosphate soaked with 5M sodium formate, 0.1M sodium acetate trihydrate, pH4.6, 50mM alpha-D-glucose 1- ...Details: 3.4M sodium formate, 0.1M sodium acetate trihydrate, pH4.6, 20mM alpha-D-glucose 1-phosphate soaked with 5M sodium formate, 0.1M sodium acetate trihydrate, pH4.6, 50mM alpha-D-glucose 1-phosphate, 50mM glucose, 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: 2.4→19.95 Å / Num. all: 66271 / Num. obs: 54077 / % possible obs: 81.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.33 Å2
Reflection shellResolution: 2.4→2.53 Å / % possible all: 81.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.95 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.32 / σ(F): 0 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2815 2571 5.04 %random
Rwork0.2311 ---
all0.2337 50972 --
obs0.2337 50972 77.31 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.616 Å2 / ksol: 0.457 e/Å3
Displacement parametersBiso max: 161.67 Å2 / Biso mean: 21.6501 Å2 / Biso min: 0.43 Å2
Baniso -1Baniso -2Baniso -3
1--4.7892 Å20 Å20.1208 Å2
2--4.0261 Å2-0 Å2
3---0.7631 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12875 0 48 628 13551
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613278
X-RAY DIFFRACTIONf_angle_d1.07118108
X-RAY DIFFRACTIONf_chiral_restr0.0611929
X-RAY DIFFRACTIONf_plane_restr0.0052398
X-RAY DIFFRACTIONf_dihedral_angle_d15.0454698
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B6395X-RAY DIFFRACTIONPOSITIONAL0.154
12A6395X-RAY DIFFRACTIONPOSITIONAL0.154
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 (%)
2.4-2.48570.38312350.31364161439667
2.4857-2.5850.34372450.28664756500176
2.585-2.70240.32532660.27284739500577
2.7024-2.84450.30192530.25514931518478
2.8445-3.02210.29182460.24714989523580
3.0221-3.25450.28942690.23454978524780
3.2545-3.58040.24872750.20444970524580
3.5804-4.09460.25192650.19135034529980
4.0946-5.1440.22892450.18125003524879
5.144-19.950.282720.24784840511276

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