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- PDB-1ayx: CRYSTAL STRUCTURE OF GLUCOAMYLASE FROM SACCHAROMYCOPSIS FIBULIGER... -

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Basic information

Entry
Database: PDB / ID: 1ayx
TitleCRYSTAL STRUCTURE OF GLUCOAMYLASE FROM SACCHAROMYCOPSIS FIBULIGERA AT 1.7 ANGSTROMS
ComponentsGLUCOAMYLASEGlucan 1,4-a-glucosidase
KeywordsHYDROLASE / GLUCOAMYLASE / GLYCOSIDASE / POLYSACCHARIDE DEGRADATION
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / polysaccharide catabolic process
Similarity search - Function
Glucoamylase / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomycopsis fibuligera (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSevcik, J. / Hostinova, E. / Gasperik, J. / Solovicova, A. / Wilson, K.S. / Dauter, Z.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of glucoamylase from Saccharomycopsis fibuligera at 1.7 A resolution.
Authors: Sevcik, J. / Solovicova, A. / Hostinova, E. / Gasperik, J. / Wilson, K.S. / Dauter, Z.
History
DepositionNov 12, 1997Processing site: BNL
Revision 1.0May 13, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUCOAMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7822
Polymers54,6601
Non-polymers1221
Water7,224401
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.140, 87.790, 99.950
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 GLUCOAMYLASE / Glucan 1,4-a-glucosidase


Mass: 54659.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomycopsis fibuligera (fungus) / Gene: GLU1 / Production host: Escherichia coli (E. coli) / References: UniProt: P08017, glucan 1,4-alpha-glucosidase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growpH: 5.1
Details: 50 MM ACETATE BUFFER, PH 5.1, 15 % (W/V) PEG 8000 HANGING DROP
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 5.5 / PH range high: 4.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215-16 %(w/v)PEG80001drop
350 mMacetate1drop
430-32 %(w/v)PEG80001reservoir
5100 mMacetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 17.8 Å2
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 29 Å / Num. obs: 56654 / % possible obs: 99.4 % / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.71 Å / Mean I/σ(I) obs: 3.5

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementResolution: 1.7→30 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1157 2 %RANDOM
Rwork0.144 ---
obs0.149 56654 99.4 %-
Displacement parametersBiso mean: 19.7 Å2
Refine analyzeLuzzati d res low obs: 30 Å / Luzzati sigma a obs: 0.05 Å
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3871 0 8 401 4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.993
X-RAY DIFFRACTIONp_mcangle_it2.615
X-RAY DIFFRACTIONp_scbond_it3.756
X-RAY DIFFRACTIONp_scangle_it4.738
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1460.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.140.3
X-RAY DIFFRACTIONp_planar_tor5.27
X-RAY DIFFRACTIONp_staggered_tor15.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.120
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor all: 0.149 / Rfactor obs: 0.144
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.181 / Num. reflection Rfree: 1157 / % reflection Rfree: 2 % / Rfactor all: 0.149 / Rfactor obs: 0.144

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