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- PDB-4zlf: Cellobionic acid phosphorylase - cellobionic acid complex -

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Basic information

Entry
Database: PDB / ID: 4zlf
TitleCellobionic acid phosphorylase - cellobionic acid complex
ComponentsPutative b-glycan phosphorylase
KeywordsTRANSFERASE / (alpha/alpha)6 barrel / glycoside hydrolase family 94 / oxidative cellulose degradation system / intracellular enzyme
Function / homology
Function and homology information


hexosyltransferase activity / cellulose catabolic process / carbohydrate binding
Similarity search - Function
Cellobionic acid phosphorylase, N-terminal / 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 / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
4-O-beta-D-glucopyranosyl-D-gluconic acid / Putative b-glycan phosphorylase
Similarity search - Component
Biological speciesSaccharophagus degradans 2-40 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsNam, Y.W. / Arakawa, T. / Fushinobu, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries and Food Industry25010A Japan
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Crystal Structure and Substrate Recognition of Cellobionic Acid Phosphorylase, Which Plays a Key Role in Oxidative Cellulose Degradation by Microbes.
Authors: Nam, Y.W. / Nihira, T. / Arakawa, T. / Saito, Y. / Kitaoka, M. / Nakai, H. / Fushinobu, S.
#1: Journal: FEBS LETT. / Year: 2013
Title: Discovery of cellobionic acid phosphorylase in cellulolytic bacteria and fungi
Authors: Nihira, T. / Saito, Y. / Nishimoto, M. / Kitaoka, M. / Igarashi, K. / Ohtsubo, K. / Nakai, H.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative b-glycan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,82910
Polymers89,7831
Non-polymers1,0469
Water14,556808
1
A: Putative b-glycan phosphorylase
hetero molecules

A: Putative b-glycan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,65920
Polymers179,5662
Non-polymers2,09318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area9530 Å2
ΔGint-108 kcal/mol
Surface area51030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.189, 107.189, 186.824
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Components on special symmetry positions
IDModelComponents
11A-1382-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Putative b-glycan phosphorylase / Cellobionic acid phosphorylase


Mass: 89782.922 Da / Num. of mol.: 1 / Mutation: M1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharophagus degradans 2-40 (bacteria)
Strain: 2-40 / Gene: cep94B / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus / References: UniProt: Q21MB1, EC: 2.4.1.321
#2: Sugar ChemComp-CEZ / 4-O-beta-D-glucopyranosyl-D-gluconic acid / cellobionic acid / 4-O-beta-D-glucosyl-D-gluconic acid / 4-O-D-glucosyl-D-gluconic acid / 4-O-glucosyl-D-gluconic acid


Type: D-saccharide / Mass: 358.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22O12

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Non-polymers , 4 types, 816 molecules

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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.5 % / Description: hexagonal bypyramid
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate, 0.1 M Li2SO4, 0.6 M (NH3)2SO4, 5%(v/v) glycerol
PH range: 5.6-6.0

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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 210r / Detector: CCD / Date: Nov 10, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 163884 / % possible obs: 100 % / Redundancy: 7.9 % / Rsym value: 0.043 / Net I/σ(I): 37.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→31.14 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.267 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17722 8191 5 %RANDOM
Rwork0.15611 ---
obs0.15719 155047 99.64 %-
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: 22.972 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.6→31.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6228 0 65 809 7102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0196470
X-RAY DIFFRACTIONr_bond_other_d0.0030.025947
X-RAY DIFFRACTIONr_angle_refined_deg2.5591.9478779
X-RAY DIFFRACTIONr_angle_other_deg1.221313686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6215788
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0724.565322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.048151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.041533
X-RAY DIFFRACTIONr_chiral_restr0.1720.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0217434
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021567
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_it2.0932.0323143
X-RAY DIFFRACTIONr_mcbond_other2.0762.0313142
X-RAY DIFFRACTIONr_mcangle_it2.6053.0423928
X-RAY DIFFRACTIONr_mcangle_other2.6043.0433929
X-RAY DIFFRACTIONr_scbond_it3.6822.3383327
X-RAY DIFFRACTIONr_scbond_other3.6822.3373327
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2853.3744850
X-RAY DIFFRACTIONr_long_range_B_refined6.38418.0948172
X-RAY DIFFRACTIONr_long_range_B_other6.20717.2687694
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 613 -
Rwork0.221 11297 -
obs--99.67 %

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