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- PDB-3qde: The structure of Cellobiose phosphorylase from Clostridium thermo... -

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Basic information

Entry
Database: PDB / ID: 3qde
TitleThe structure of Cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate
ComponentsCellobiose phosphorylase
KeywordsTRANSFERASE / cellulase / cellobiose / phosphate / 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, C-terminal / Glycosyl hydrolase family 65, C-terminal 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 ...mpn423 like domain / Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal 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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / PHOSPHATE ION / Cellobiose phosphorylase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsBianchetti, C.M. / Elsen, N.L. / Horn, M.K. / Fox, B.G. / Phillips Jr., G.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of cellobiose phosphorylase from Clostridium thermocellum in complex with phosphate.
Authors: Bianchetti, C.M. / Elsen, N.L. / Fox, B.G. / Phillips, G.N.
History
DepositionJan 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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)186,4136
Polymers185,9792
Non-polymers4344
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-22 kcal/mol
Surface area50230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.262, 122.062, 181.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cellobiose phosphorylase /


Mass: 92989.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: cbp, Q8VP44 / Plasmid: pEC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8VP44, cellobiose phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein Solution (5.0 mg/ml protein, 0.05 M NaCl, 0.0003 M NaN3, and 0.005 M HEPES pH 7) mixed in a 1:1 ratio with the Well Solution (0.157 M (NH4)2HPO4, 2.143 M (NH4)H2PO4, and 0.1 M Tris ...Details: Protein Solution (5.0 mg/ml protein, 0.05 M NaCl, 0.0003 M NaN3, and 0.005 M HEPES pH 7) mixed in a 1:1 ratio with the Well Solution (0.157 M (NH4)2HPO4, 2.143 M (NH4)H2PO4, and 0.1 M Tris pH 8.0). Cryoprotected with 0.157 M (NH4)2HPO4, 2.143 M (NH4)H2PO4, 5% ethylene glycol, and 0.1 M Tris pH 8.0, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARmosaic 300 / Detector: CCD / Date: Nov 19, 2009 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 73974 / % possible obs: 99.5 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.127 / Χ2: 1.173 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.465.30.4247721.237197.6
2.46-2.525.50.39247921.273198.4
2.52-2.595.60.36348271.204198.9
2.59-2.665.80.34548571.183199.2
2.66-2.7560.31548841.17199.8
2.75-2.856.20.2949041.16199.9
2.85-2.966.50.2648961.21100
2.96-3.096.60.22849691.2021100
3.09-3.266.60.18349061.1921100
3.26-3.466.60.15249511.2441100
3.46-3.736.60.12549401.2291100
3.73-4.16.60.10549621.191100
4.1-4.76.60.09450141.0611100
4.7-5.926.50.07950561.1421100
5.92-506.20.06852440.958199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å34.33 Å
Translation2.5 Å34.33 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→34.326 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.29 / σ(F): 0 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 3535 4.99 %
Rwork0.1508 --
obs0.1536 70898 95.02 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.296 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 103.79 Å2 / Biso mean: 34.1839 Å2 / Biso min: 16.35 Å2
Baniso -1Baniso -2Baniso -3
1--4.0662 Å20 Å20 Å2
2--3.8791 Å2-0 Å2
3---0.1871 Å2
Refinement stepCycle: LAST / Resolution: 2.4→34.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13126 0 26 692 13844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613537
X-RAY DIFFRACTIONf_angle_d0.93318314
X-RAY DIFFRACTIONf_chiral_restr0.0691867
X-RAY DIFFRACTIONf_plane_restr0.0032384
X-RAY DIFFRACTIONf_dihedral_angle_d13.9914958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3846-2.41730.24491060.19732082218875
2.4173-2.45180.26771280.19482492262088
2.4518-2.48840.29281320.19032470260289
2.4884-2.52730.26851400.18722531267190
2.5273-2.56870.26451310.1812533266491
2.5687-2.6130.24921330.1912598273192
2.613-2.66050.25181350.1912581271692
2.6605-2.71160.27391340.20182635276993
2.7116-2.7670.27681390.20682621276094
2.767-2.82710.31561400.19372635277594
2.8271-2.89280.24191390.18842685282494
2.8928-2.96510.27261390.19012689282895
2.9651-3.04530.25821440.18462709285396
3.0453-3.13480.2451480.18042737288597
3.1348-3.23590.22231460.16862736288298
3.2359-3.35150.22211410.16782787292898
3.3515-3.48550.21821460.15792800294699
3.4855-3.6440.1971470.15272814296199
3.644-3.83590.18371490.12622817296699
3.8359-4.07590.16171490.12172832298199
4.0759-4.390.16031520.10962869302199
4.39-4.83070.1551490.10628442993100
4.8307-5.52720.17281530.110829073060100
5.5272-6.95420.17291540.135529223076100
6.9542-34.32940.17691610.14330373198100

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