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- PDB-3wir: Crystal structure of kojibiose phosphorylase complexed with glucose -

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Basic information

Entry
Database: PDB / ID: 3wir
TitleCrystal structure of kojibiose phosphorylase complexed with glucose
ComponentsKojibiose phosphorylase
KeywordsTRANSFERASE / (alpha/alpha)6 barrel / Phosphorylase
Function / homology
Function and homology information


kojibiose phosphorylase / kojibiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Maltose phosphorylase/glycosyl hydrolase/vacuolar acid trehalase / Glycoside hydrolase, family 65, central catalytic / Glycoside hydrolase, family 65, N-terminal / Glycosyl hydrolase family 65 central catalytic domain / Glycosyl hydrolase family 65, N-terminal domain / Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 ...Maltose phosphorylase/glycosyl hydrolase/vacuolar acid trehalase / Glycoside hydrolase, family 65, central catalytic / Glycoside hydrolase, family 65, N-terminal / Glycosyl hydrolase family 65 central catalytic domain / Glycosyl hydrolase family 65, N-terminal domain / Glycoside hydrolase family 65, C-terminal / Glycosyl hydrolase family 65, C-terminal domain / Glycoside hydrolase, family 65, N-terminal domain / Maltose phosphorylase, domain 3 / Maltose phosphorylase, domain 3 / Glycoside hydrolase family 65, N-terminal domain superfamily / Glycosyltransferase - #10 / Beta-galactosidase; Chain A, domain 5 / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-D-glucopyranose / PHOSPHATE ION / Kojibiose phosphorylase
Similarity search - Component
Biological speciesCaldicellulosiruptor saccharolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsOkada, S. / Yamamoto, T. / Watanabe, H. / Nishimoto, T. / Chaen, H. / Fukuda, S. / Wakagi, T. / Fushinobu, S.
Citation
Journal: Febs J. / Year: 2014
Title: Structural and mutational analysis of substrate recognition in kojibiose phosphorylase
Authors: Okada, S. / Yamamoto, T. / Watanabe, H. / Nishimoto, T. / Chaen, H. / Fukuda, S. / Wakagi, T. / Fushinobu, S.
#1: Journal: Biosci.Biotechnol.Biochem. / Year: 2011
Title: Enzymatic properties of recombinant kojibiose phosphorylase from Caldicellulosiruptor saccharolyticus ATCC43494
Authors: Yamamoto, T. / Nishio-Kosaka, M. / Izawa, S. / Aga, H. / Nishimoto, T. / Chaen, H. / Fukuda, S.
History
DepositionSep 24, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 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
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Kojibiose phosphorylase
B: Kojibiose phosphorylase
C: Kojibiose phosphorylase
D: Kojibiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,58327
Polymers354,7434
Non-polymers2,84023
Water24,8251378
1
A: Kojibiose phosphorylase
C: Kojibiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,74513
Polymers177,3722
Non-polymers1,37411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kojibiose phosphorylase
D: Kojibiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,83814
Polymers177,3722
Non-polymers1,46612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.581, 104.464, 124.164
Angle α, β, γ (deg.)68.83, 86.02, 90.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Kojibiose phosphorylase /


Mass: 88685.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor saccharolyticus (bacteria)
Strain: ATCC 43494 / DSM 8903 / Gene: Csac_0444 / Plasmid: pRSET0439-C-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL / References: UniProt: A4XGP2, kojibiose phosphorylase
#2: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 8
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1378 / 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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 5mM D-glucose, 5mM sodium phosphate, 10%(v/v) 2-propanol, 10%(w/v) PEG3350, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2011
RadiationMonochromator: Fixed exit double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 209616 / Num. obs: 203954 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.097 / Net I/σ(I): 14.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 22589 / Rsym value: 0.46 / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H54

1h54


Resolution: 2.05→46.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.21 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25055 10235 5 %RANDOM
Rwork0.19072 ---
all0.19371 199809 --
obs0.19374 193715 96.95 %-
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: 31.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0.02 Å20.02 Å2
2---0.04 Å20.05 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24748 0 180 1378 26306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01925478
X-RAY DIFFRACTIONr_bond_other_d0.0010.0224180
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9634419
X-RAY DIFFRACTIONr_angle_other_deg0.874355764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.87553020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36624.9371264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.995154612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.02315108
X-RAY DIFFRACTIONr_chiral_restr0.1110.23717
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0228508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025880
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.048→2.101 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 693 -
Rwork0.25 13615 -
obs--91.83 %

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