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- PDB-1lf6: CRYSTAL STRUCTURE OF BACTERIAL GLUCOAMYLASE -

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Basic information

Entry
Database: PDB / ID: 1lf6
TitleCRYSTAL STRUCTURE OF BACTERIAL GLUCOAMYLASE
Componentsglucoamylase
KeywordsHYDROLASE / (alpha/alpha) barrel / 6 alpha-helical hairpin torroid / super beta sandwich / carbohydrase family GH15
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / glycosyltransferase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glucoamylase, bacterial / Glucodextranase, N-terminal / Glucodextranase, domain N / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Beta-galactosidase; Chain A, domain 5 - #10 / Glycosyltransferase - #10 / Glycoside hydrolase-type carbohydrate-binding ...Glucoamylase, bacterial / Glucodextranase, N-terminal / Glucodextranase, domain N / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Beta-galactosidase; Chain A, domain 5 - #10 / Glycosyltransferase - #10 / Glycoside hydrolase-type carbohydrate-binding / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesThermoanaerobacterium thermosaccharolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAleshin, A.E. / Feng, P.-H. / Honzatko, R.B. / Reilly, P.J.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure and evolution of prokaryotic glucoamylase
Authors: Aleshin, A.E. / Feng, P.-H. / Honzatko, R.B. / Reilly, P.J.
History
DepositionApr 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Author states the sequence of this crystal structure differs from the DNA sequence of ...SEQUENCE Author states the sequence of this crystal structure differs from the DNA sequence of GenBank entry AAC24003. The crystal structure has insertions at residue 125 and after residue 679. These differences are consistent with Genbank entry BAA02251.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glucoamylase
B: glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,3734
Polymers153,1812
Non-polymers1922
Water16,358908
1
A: glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6872
Polymers76,5911
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6872
Polymers76,5911
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.186, 102.513, 164.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2
DetailsThe presumable biological assembly is a monomer, but the crystallographically observed dimer may also be functional

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Components

#1: Protein glucoamylase / GLUCAN 1 / 4-ALPHA-GLUCOSIDASE / 1 / 4-ALPHA-D-GLUCAN GLUCOHYDROLASE / AMYLOGLUCOSIDASE / GAMMA- ...GLUCAN 1 / 4-ALPHA-GLUCOSIDASE / 1 / 4-ALPHA-D-GLUCAN GLUCOHYDROLASE / AMYLOGLUCOSIDASE / GAMMA-AMYLASE / LYSOSOMAL ALPHA-GLUCOSIDASE / EXO-1 / 4-ALPHA-GLUCOSIDASE


Mass: 76590.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermoanaerobacterium thermosaccharolyticum (bacteria)
Strain: DSM 571 / References: UniProt: O85672, glucan 1,4-alpha-glucosidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 908 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, Tris-HCl, Lithium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 24K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH7.5
214-16 %PEG33501reservoir
3100 mMTris-HCl1reservoirpH8.0
4200 mM1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.01 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2001 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 80922 / Num. obs: 76199 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 38.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.07 / % possible all: 82
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / % possible obs: 90 % / Num. measured all: 446637
Reflection shell
*PLUS
% possible obs: 82 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.69 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3080144.38 / Data cutoff high rms absF: 3080144.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 5360 7.1 %RANDOM
Rwork0.194 ---
all0.1969 75429 --
obs-75429 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6441 Å2 / ksol: 0.369351 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.66 Å20 Å20 Å2
2--8.3 Å20 Å2
3----4.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10666 0 10 908 11584
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it2.872.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight Biso Weight position
11RESTRAINX-RAY DIFFRACTION0.15830
22X-RAY DIFFRACTION0.24830
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 744 7.1 %
Rwork0.203 9762 -
obs--78.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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