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- PDB-3qfy: Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase C... -

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Basic information

Entry
Database: PDB / ID: 3qfy
TitleCrystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase Complexed with Sulfate and Isofagomine
ComponentsCellobiose Phosphorylase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Alpha(6)/Alpha(6) Barrel / Phosphorylase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36 superfamily, 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 / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycosyl hydrolase 36, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / cAMP-dependent Protein Kinase, Chain A / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase 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 / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Cellobiose Phosphorylase
Similarity search - Component
Biological speciesCellvibrio gilvus (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsFushinobu, S. / Hidaka, M. / Hayashi, A.M. / Wakagi, T. / Shoun, H. / Kitaoka, M.
CitationJournal: J.Appl.Glyosci. / Year: 2011
Title: Interactions between glycoside hydrolase family 94 cellobiose phosphorylase and glucosidase inhibitors
Authors: Fushinobu, S. / Hidaka, M. / Hayashi, A.M. / Wakagi, T. / Shoun, H. / Kitaoka, M.
History
DepositionJan 24, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Non-polymer description
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 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.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _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)187,51712
Polymers186,1442
Non-polymers1,37310
Water20,5911143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-13 kcal/mol
Surface area48720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.710, 98.254, 104.450
Angle α, β, γ (deg.)90.00, 102.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Cellobiose Phosphorylase /


Mass: 93071.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio gilvus (unknown) / Strain: ATCC 13127 / 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

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Non-polymers , 4 types, 1151 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL / Afegostat


Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1143 / 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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M ammonium sulfate, 0.1M HEPES-NaOH, 10mM glucose, 1mM isofagomine, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2007
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 74250 / Num. obs: 74187 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.109 / Net I/σ(I): 13
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 7391 / Rsym value: 0.326 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→38.32 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.802 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20839 3725 5 %RANDOM
Rwork0.13767 ---
obs0.14121 70349 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.473 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å21.07 Å2
2--0.7 Å20 Å2
3---0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.219 Å0.324 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12856 0 84 1143 14083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02213287
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.94218132
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79351642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46423.772668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.701151920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2181592
X-RAY DIFFRACTIONr_chiral_restr0.1150.21918
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02110544
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_it0.8361.58158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.497213098
X-RAY DIFFRACTIONr_scbond_it2.70835129
X-RAY DIFFRACTIONr_scangle_it4.0924.55034
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 262 -
Rwork0.164 5161 -
obs--98.73 %

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