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- PDB-5b0q: beta-1,2-Mannobiose phosphorylase from Listeria innocua - mannose... -

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Basic information

Entry
Database: PDB / ID: 5b0q
Titlebeta-1,2-Mannobiose phosphorylase from Listeria innocua - mannose complex
ComponentsLin0857 protein
KeywordsTRANSFERASE / Glycoside phosphorylase
Function / homologybeta-1,2-mannobiose phosphorylase / Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / glycosyltransferase activity / alpha-D-mannopyranose / Beta-1,2-mannobiose phosphorylase
Function and homology information
Biological speciesListeria innocua Clip11262 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTsuda, T. / Arakawa, T. / Fushinobu, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
The Ministry of Agriculture, Forestry and Fisheries, Japan25010A Japan
CitationJournal: Febs Lett. / Year: 2015
Title: Characterization and crystal structure determination of beta-1,2-mannobiose phosphorylase from Listeria innocua
Authors: Tsuda, T. / Nihira, T. / Chiku, K. / Suzuki, E. / Arakawa, T. / Nishimoto, M. / Kitaoka, M. / Nakai, H. / Fushinobu, S.
History
DepositionNov 2, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 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

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Assembly

Deposited unit
A: Lin0857 protein
B: Lin0857 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1609
Polymers82,2202
Non-polymers9407
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-71 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.212, 146.212, 105.841
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Lin0857 protein / beta-1 / 2-Mannobiose phosphorylase


Mass: 41110.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua Clip11262 (bacteria) / Strain: CLIP 11262 / Gene: lin0857 / Plasmid: pET24a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3)-RIL / References: UniProt: Q92DF6
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 4.01 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 1.8 M (NH4)2SO4, 10 mM CoCl2, 0.1 M MES-NaOH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 15, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 58114 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 22.7
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 3.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VKD

1vkd


Resolution: 2.3→47.86 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.152 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21719 2942 5.1 %RANDOM
Rwork0.17153 ---
obs0.1738 55135 99.6 %-
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: 39.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.168 Å0.177 Å
Refinement stepCycle: 1 / Resolution: 2.3→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5625 0 56 346 6027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195813
X-RAY DIFFRACTIONr_bond_other_d0.0020.025396
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.9757885
X-RAY DIFFRACTIONr_angle_other_deg1.142312460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7085705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10424.514288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66415954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2071530
X-RAY DIFFRACTIONr_chiral_restr0.150.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216561
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021317
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_it3.4093.6942826
X-RAY DIFFRACTIONr_mcbond_other3.4053.6942825
X-RAY DIFFRACTIONr_mcangle_it4.4665.5323529
X-RAY DIFFRACTIONr_mcangle_other4.4675.5333530
X-RAY DIFFRACTIONr_scbond_it4.2884.1432987
X-RAY DIFFRACTIONr_scbond_other4.2874.1432987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2696.0344357
X-RAY DIFFRACTIONr_long_range_B_refined7.51129.5066361
X-RAY DIFFRACTIONr_long_range_B_other7.51129.5066361
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.299→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 217 -
Rwork0.222 3876 -
obs--95.7 %

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