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- PDB-1xsk: Structure of a Family 31 alpha glycosidase glycosyl-enzyme interm... -

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Basic information

Entry
Database: PDB / ID: 1xsk
TitleStructure of a Family 31 alpha glycosidase glycosyl-enzyme intermediate
ComponentsPutative family 31 glucosidase yicI
KeywordsHYDROLASE / beta(8)alpha(8) barrel and beta sandwich domains
Function / homology
Function and homology information


xyloglucan 1,6-alpha-xylosidase activity / alpha-D-xyloside xylohydrolase / alpha-D-xyloside xylohydrolase / carbohydrate binding / carbohydrate metabolic process / identical protein binding
Similarity search - Function
: / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II ...: / glycosyl hydrolase (family 31) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5(R)-fluoro-beta-D-xylopyranose / Alpha-xylosidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLovering, A.L. / Lee, S.S. / Kim, Y.W. / Withers, S.G. / Strynadka, N.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Mechanistic and Structural Analysis of a Family 31 {alpha}-Glycosidase and Its Glycosyl-enzyme Intermediate
Authors: Lovering, A.L. / Lee, S.S. / Kim, Y.W. / Withers, S.G. / Strynadka, N.C.
History
DepositionOct 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative family 31 glucosidase yicI
B: Putative family 31 glucosidase yicI
C: Putative family 31 glucosidase yicI
D: Putative family 31 glucosidase yicI
E: Putative family 31 glucosidase yicI
F: Putative family 31 glucosidase yicI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)536,76627
Polymers534,0126
Non-polymers2,75421
Water15,259847
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26920 Å2
ΔGint-242 kcal/mol
Surface area145710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.142, 175.465, 210.854
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative family 31 glucosidase yicI


Mass: 89002.023 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yicI / Production host: Escherichia coli (E. coli)
References: UniProt: P31434, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Sugar
ChemComp-XYF / 5(R)-fluoro-beta-D-xylopyranose / 5(R)-fluoro-beta-D-xylose / 5(R)-fluoro-D-xylose / 5(R)-fluoro-xylose


Type: D-saccharide, beta linking / Mass: 167.112 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H8FO5
#4: Chemical
ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM sodium acetate, 2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 303936 / Num. obs: 296995 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.406 / % possible all: 94.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1XSI

1xsi


Resolution: 2.2→29.88 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5562235.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 14564 4.9 %RANDOM
Rwork0.235 ---
all0.235 303936 --
obs0.235 296995 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.4018 Å2 / ksol: 0.354166 e/Å3
Displacement parametersBiso mean: 33.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.44 Å20 Å20 Å2
2---9.53 Å20 Å2
3---10.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms37356 0 157 847 38360
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 2351 4.8 %
Rwork0.304 46142 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3XYF_AT14.PARAMXYF_AT14.TOP
X-RAY DIFFRACTION4MOPS_ALT.PARAMMOPS_ALT.TOP
X-RAY DIFFRACTION5SO4_ALT.PARAMSO4_ALT.TOP

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