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- PDB-4zli: Cellobionic acid phosphorylase - 3-O-beta-D-glucopyranosyl-alpha-... -

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Basic information

Entry
Database: PDB / ID: 4zli
TitleCellobionic acid phosphorylase - 3-O-beta-D-glucopyranosyl-alpha-D-glucopyranuronic 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 / Glycosyl hydrolase 94, supersandwich domain / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 94 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
Putative b-glycan phosphorylase
Similarity search - Component
Biological speciesSaccharophagus degradans 2-40 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 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

Downloads & links

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Assembly

Deposited unit
A: Putative b-glycan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,01912
Polymers89,7831
Non-polymers1,23611
Water11,331629
1
A: Putative b-glycan phosphorylase
hetero molecules

A: Putative b-glycan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,03924
Polymers179,5662
Non-polymers2,47322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area6530 Å2
ΔGint-99 kcal/mol
Surface area51190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.058, 107.058, 185.767
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-1328-

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: Polysaccharide beta-D-glucopyranose-(1-3)-alpha-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 356.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpAa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122A-1a_1-5][a2122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpA]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 639 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 629 / 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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate (pH 5.6-6.0), 0.1 M Li2SO4, 0.6 M (NH3)2SO4, and 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: BL-17A / Wavelength: 0.9732 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 29, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9732 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 114626 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rsym value: 0.092 / Net I/σ(I): 24.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 4.1 / % 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: 1.8→40.5 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.895 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18801 5709 5 %RANDOM
Rwork0.15473 ---
obs0.15638 108205 99.44 %-
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: 28.168 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6228 0 75 629 6932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0196459
X-RAY DIFFRACTIONr_bond_other_d0.0030.025930
X-RAY DIFFRACTIONr_angle_refined_deg2.2271.958764
X-RAY DIFFRACTIONr_angle_other_deg1.16313646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165784
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33524.594320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.489151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0471533
X-RAY DIFFRACTIONr_chiral_restr0.1580.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217406
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021555
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_it2.6192.5773139
X-RAY DIFFRACTIONr_mcbond_other2.6122.5753138
X-RAY DIFFRACTIONr_mcangle_it3.0693.8483922
X-RAY DIFFRACTIONr_mcangle_other3.0693.8493923
X-RAY DIFFRACTIONr_scbond_it3.942.8943320
X-RAY DIFFRACTIONr_scbond_other3.9142.8883301
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5874.1934817
X-RAY DIFFRACTIONr_long_range_B_refined6.53721.8277860
X-RAY DIFFRACTIONr_long_range_B_other6.44121.2987544
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 411 -
Rwork0.207 8008 -
obs--99.83 %

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