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- PDB-5ghl: Crystal structure Analysis of the starch-binding domain of glucoa... -

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Basic information

Entry
Database: PDB / ID: 5ghl
TitleCrystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus niger
ComponentsGlucoamylaseGlucan 1,4-a-glucosidase
KeywordsHYDROLASE / beta-sheet structure
Function / homology
Function and homology information


polysaccharide metabolic process / glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / starch binding / fungal-type vacuole / polysaccharide catabolic process / endoplasmic reticulum
Similarity search - Function
Glucoamylase, starch-binding / Glucoamylase, CBM20 domain / Glucoamylase / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. ...Glucoamylase, starch-binding / Glucoamylase, CBM20 domain / Glucoamylase / : / Glucoamylase active site region signature. / GH15-like domain / Glycosyl hydrolases family 15 / Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiyake, H. / Suyama, Y. / Muraki, N. / Kusunoki, M. / Tanaka, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2017
Title: Crystal structure of the starch-binding domain of glucoamylase from Aspergillus niger.
Authors: Suyama, Y. / Muraki, N. / Kusunoki, M. / Miyake, H.
History
DepositionJun 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucoamylase
B: Glucoamylase
C: Glucoamylase
D: Glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,29212
Polymers47,5394
Non-polymers7538
Water3,675204
1
A: Glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0733
Polymers11,8851
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0733
Polymers11,8851
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0733
Polymers11,8851
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0733
Polymers11,8851
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.360, 75.360, 91.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
Glucoamylase / Glucan 1,4-a-glucosidase / 1 / 4-alpha-D-glucan glucohydrolase / Glucan 1 / 4-alpha-glucosidase


Mass: 11884.820 Da / Num. of mol.: 4
Fragment: UNP residues 533-640, starch-binding domain of glucoamylase from Aspergillus niger
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Gene: GLAA / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P69328, glucan 1,4-alpha-glucosidase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulfate, PEG400, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34419 / % possible obs: 99.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.107 / Χ2: 20.38 / Net I/σ(I): 44.5 / Num. measured all: 291560
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.038.20.164171010.4371100
2.03-2.078.50.161171311.2951100
2.07-2.118.50.152171112.5361100
2.11-2.158.50.149173813.3891100
2.15-2.28.50.149167915.0781100
2.2-2.258.50.146171916.0051100
2.25-2.318.50.144172816.061100
2.31-2.378.50.141172017.3751100
2.37-2.448.50.135169917.4211100
2.44-2.528.50.14174220.8241100
2.52-2.618.60.128169720.4891100
2.61-2.718.50.132172024.0761100
2.71-2.848.50.125171624.6531100
2.84-2.998.60.12171625.7581100
2.99-3.178.50.114173625.9361100
3.17-3.428.50.112172729.2361100
3.42-3.768.50.104172929.6841100
3.76-4.318.50.097171628.835199.9
4.31-5.438.30.088175426.818199.9
5.43-507.90.077174920.891198.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data collection
SCALEPACKdata scaling
Cootmodel building
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NYI

3nyi


Resolution: 2→45.98 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.052 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 1716 5 %RANDOM
Rwork0.1783 ---
obs0.1809 32650 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.6 Å2 / Biso mean: 25.954 Å2 / Biso min: 7.83 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 44 204 3599
Biso mean--50.82 33.81 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023475
X-RAY DIFFRACTIONr_bond_other_d0.0010.022984
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.9424778
X-RAY DIFFRACTIONr_angle_other_deg1.01636916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6815428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78424.865148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51615488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7181512
X-RAY DIFFRACTIONr_chiral_restr0.150.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023876
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 106 -
Rwork0.2 2401 -
all-2507 -
obs--100 %

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