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- PDB-5a7v: The GH130 family of mannoside phosphorylases contains glycoside h... -

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Basic information

Entry
Database: PDB / ID: 5a7v
TitleThe GH130 family of mannoside phosphorylases contains glycoside hydrolases that target beta-1,2 mannosidic linkages in Candida mannan
Components(PUTATIVE GLYCOSIDASE PH117- ...) x 2
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / PHOSPHORYLASE / CELL WALL / YEAST
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / glycosyltransferase activity / carbohydrate metabolic process
Similarity search - Function
Mannoside phosphorylase / beta-1,4-mannooligosaccharide phosphorylase / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-D-mannopyranose / Glycosidase, PH117-related / Putative glycosidase PH117-related
Similarity search - Component
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsCuskin, F. / Basle, A. / Day, A.M. / Ladeveze, S. / Potocki-Veronese, G. / Davies, G.J. / Gilbert, H.J. / Lowe, E.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Gh130 Family of Mannoside Phosphorylases Contains Glycoside Hydrolases that Target Beta-1,2 Mannosidic Linkages in Candida Mannan
Authors: Cuskin, F. / Basle, A. / Day, A.M. / Ladeveze, S. / Potocki-Veronese, G. / Davies, G.J. / Gilbert, H.J. / Lowe, E.
History
DepositionJul 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: 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: PUTATIVE GLYCOSIDASE PH117-RELATED
B: PUTATIVE GLYCOSIDASE PH117-RELATED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,93918
Polymers86,8972
Non-polymers2,04216
Water15,439857
1
A: PUTATIVE GLYCOSIDASE PH117-RELATED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,54210
Polymers43,4261
Non-polymers1,1179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE GLYCOSIDASE PH117-RELATED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3968
Polymers43,4721
Non-polymers9257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.767, 118.110, 126.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-2462-

HOH

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Components

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PUTATIVE GLYCOSIDASE PH117- ... , 2 types, 2 molecules AB

#1: Protein PUTATIVE GLYCOSIDASE PH117-RELATED / GH130


Mass: 43425.648 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: R7KJA6, UniProt: Q8A186*PLUS
#2: Protein PUTATIVE GLYCOSIDASE PH117-RELATED / GH130


Mass: 43471.734 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: R7KJA6, UniProt: Q8A186*PLUS

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Sugars , 2 types, 6 molecules

#3: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
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

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Non-polymers , 2 types, 867 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 3.4 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growDetails: 2.2 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.35→46.58 Å / Num. obs: 243880 / % possible obs: 98.3 % / Observed criterion σ(I): 1.8 / Redundancy: 3.4 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.7
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QC2

3qc2


Resolution: 1.35→118.11 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.38 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-16 IN CHAIN A AND 1-25 IN CHAIN B ARE DISORDERED DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1497 12016 4.99 %RANDOM
Rwork0.13 ---
obs0.131 243787 98.193 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.802 Å20 Å20 Å2
2---0.507 Å20 Å2
3----0.295 Å2
Refinement stepCycle: LAST / Resolution: 1.35→118.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5767 0 122 857 6746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.026227
X-RAY DIFFRACTIONr_bond_other_d0.0020.025644
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9628508
X-RAY DIFFRACTIONr_angle_other_deg1.028313092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3975781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0723.849291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60315978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4521532
X-RAY DIFFRACTIONr_chiral_restr0.2090.2897
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021473
X-RAY DIFFRACTIONr_nbd_refined0.2460.23784
X-RAY DIFFRACTIONr_nbd_other0.2060.2111
X-RAY DIFFRACTIONr_nbtor_refined0.1780.25622
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.110.2332
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_it1.751.3832962
X-RAY DIFFRACTIONr_mcbond_other1.7311.3812961
X-RAY DIFFRACTIONr_mcangle_it2.2532.0873713
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6471.6943265
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0452.4314767
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.8311870
X-RAY DIFFRACTIONr_sphericity_free32.2845240
X-RAY DIFFRACTIONr_sphericity_bonded12.19812291
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 905 -
Rwork0.232 17096 -
obs--98.793 %

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