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- PDB-3acs: Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase W... -

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Basic information

Entry
Database: PDB / ID: 3acs
TitleCrystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase W488F mutant
ComponentsCellobiose Phosphorylase
KeywordsTRANSFERASE / beta-sandwich / (alpha/alpha)6 barrel / phosphorylase / glycoside hydrolase family 94
Function / homology
Function and homology information


glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Cellobiose phosphorylase, N-terminal / mpn423 like domain / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Glycosyltransferase family 36 / Glycosyl hydrolase 94 / Glycosyl hydrolase 36, catalytic domain ...Cellobiose phosphorylase, N-terminal / mpn423 like domain / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Glycosyltransferase family 36 / Glycosyl hydrolase 94 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / cAMP-dependent Protein Kinase, Chain A / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Galactose mutarotase-like domain superfamily / Beta-galactosidase; Chain A, domain 5 / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-D-glucopyranose / Cellobiose Phosphorylase
Similarity search - Component
Biological speciesCellvibrio gilvus (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsHidaka, M. / Arai, T. / Fushinobu, S.
Citation
Journal: To be Published
Title: Engineering of cellobiose phosphorylase
Authors: Arai, T. / Hayashi, M.A. / Hidaka, M. / Kitaoka, M. / Wakagi, T. / Shoun, H. / Fushinobu, S.
#1: Journal: Biochem.J. / Year: 2006
Title: Structural dissection of the reaction mechanism of cellobiose phosphorylase
Authors: Hidaka, M. / Kitaoka, M. / Hayashi, K. / Wakagi, T. / Shoun, H. / Fushinobu, S.
History
DepositionJan 8, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellobiose Phosphorylase
B: Cellobiose Phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,6186
Polymers186,0662
Non-polymers5524
Water14,880826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-12 kcal/mol
Surface area48920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.796, 98.139, 104.376
Angle α, β, γ (deg.)90.00, 102.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cellobiose Phosphorylase /


Mass: 93032.766 Da / Num. of mol.: 2 / Mutation: W488F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio gilvus (unknown) / Strain: ATCC13127 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66264, cellobiose phosphorylase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 826 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: ammonium sulfate, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 57216 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.89 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CQS
Resolution: 2.51→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.926 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21129 2893 5.1 %RANDOM
Rwork0.14204 ---
obs0.14555 54155 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.227 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20.72 Å2
2--0.45 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.51→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12850 0 34 826 13710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02213232
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.93818054
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51651642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49223.772668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.123151920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.31592
X-RAY DIFFRACTIONr_chiral_restr0.1040.21912
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110538
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7081.58154
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.354213094
X-RAY DIFFRACTIONr_scbond_it2.3835078
X-RAY DIFFRACTIONr_scangle_it3.8024.54960
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.506→2.571 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 212 -
Rwork0.186 3723 -
obs--93.38 %

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