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- PDB-4zle: Cellobionic acid phosphorylase - ligand free structure -

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Basic information

Entry
Database: PDB / ID: 4zle
TitleCellobionic acid phosphorylase - ligand free structure
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: 2.1 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 1.4Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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)90,67111
Polymers89,7831
Non-polymers88810
Water8,593477
1
A: Putative b-glycan phosphorylase
hetero molecules

A: Putative b-glycan phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,34222
Polymers179,5662
Non-polymers1,77620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_465y-1,x+1,-z1
Buried area7530 Å2
ΔGint-160 kcal/mol
Surface area51350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.934, 106.934, 185.345
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-1275-

HOH

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Components

#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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 477 / 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: sodium citrate, Li2SO4, 0.6 M (NH3)2SO4, 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: 0.9988 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 12, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9988 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 72225 / % possible obs: 99.5 % / Redundancy: 7.3 % / Rsym value: 0.112 / Net I/σ(I): 17.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.6 / % 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: 2.1→41.44 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.147 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21936 3385 5.1 %RANDOM
Rwork0.17012 ---
obs0.17258 63592 92.79 %-
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: 30.548 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6224 0 49 477 6750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0196428
X-RAY DIFFRACTIONr_bond_other_d0.0020.025903
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.9458724
X-RAY DIFFRACTIONr_angle_other_deg1.068313576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9635783
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60424.594320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.286151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7451533
X-RAY DIFFRACTIONr_chiral_restr0.1210.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217395
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021554
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_it2.4962.8493135
X-RAY DIFFRACTIONr_mcbond_other2.492.8483134
X-RAY DIFFRACTIONr_mcangle_it3.3854.263917
X-RAY DIFFRACTIONr_mcangle_other3.3844.2613918
X-RAY DIFFRACTIONr_scbond_it3.4683.1453292
X-RAY DIFFRACTIONr_scbond_other3.4673.1453292
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1544.5924807
X-RAY DIFFRACTIONr_long_range_B_refined6.48723.4237727
X-RAY DIFFRACTIONr_long_range_B_other6.48723.4247728
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 163 -
Rwork0.217 2762 -
obs--55.9 %

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