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- PDB-6fhw: Structure of Hormoconis resinae Glucoamylase -

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Basic information

Entry
Database: PDB / ID: 6fhw
TitleStructure of Hormoconis resinae Glucoamylase
ComponentsGlucoamylase P
KeywordsHYDROLASE / glycosylation / starch degradation / glycoside hydrolase
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / starch binding / polysaccharide catabolic process / extracellular region
Similarity search - Function
Glucoamylase, starch-binding / Glucoamylase, CBM20 domain / Glucoamylase / 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 ...Glucoamylase, starch-binding / Glucoamylase, CBM20 domain / Glucoamylase / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-acarbose / Glucoamylase P
Similarity search - Component
Biological speciesAmorphotheca resinae (creosote fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsRoth, C. / Moroz, O.V. / Ariza, A. / Friis, E.P. / Davies, G.J. / Wilson, K.S.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structural insight into industrially relevant glucoamylases: flexible positions of starch-binding domains.
Authors: Roth, C. / Moroz, O.V. / Ariza, A. / Skov, L.K. / Ayabe, K. / Davies, G.J. / Wilson, K.S.
History
DepositionJan 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucoamylase P
B: Glucoamylase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,40616
Polymers132,9422
Non-polymers6,46414
Water0
1
A: Glucoamylase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1679
Polymers66,4711
Non-polymers3,6968
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucoamylase P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2387
Polymers66,4711
Non-polymers2,7686
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.975, 149.827, 192.349
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 66470.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amorphotheca resinae (creosote fungus) / Gene: GAMP / Production host: Trichoderma reesei QM6a (fungus) / References: UniProt: Q03045, glucan 1,4-alpha-glucosidase
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.6→59.58 Å / Num. obs: 38033 / % possible obs: 81.6 % / Redundancy: 6.5 % / Rrim(I) all: 0.142 / Net I/σ(I): 10.5
Reflection shellResolution: 3.6→3.76 Å / Rrim(I) all: 0.675

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GLM

1glm


Resolution: 3.6→59.58 Å / Cor.coef. Fo:Fc: 0.82 / Cor.coef. Fo:Fc free: 0.797 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.559
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 1887 5.1 %RANDOM
Rwork0.2642 ---
obs0.2647 35198 79.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.24 Å2 / Biso mean: 54.06 Å2 / Biso min: 31.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å2-0 Å20 Å2
2---0.6 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 3.6→59.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8956 0 429 0 9385
Biso mean--71.92 --
Num. residues----1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.029663
X-RAY DIFFRACTIONr_bond_other_d00.028330
X-RAY DIFFRACTIONr_angle_refined_deg1.2231.98713278
X-RAY DIFFRACTIONr_angle_other_deg3.864319424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44851170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6324.625413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.746151305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8731538
X-RAY DIFFRACTIONr_chiral_restr0.0680.21538
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110694
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021951
X-RAY DIFFRACTIONr_mcbond_it0.7855.5334689
X-RAY DIFFRACTIONr_mcbond_other0.7855.5324688
X-RAY DIFFRACTIONr_mcangle_it1.4358.2965856
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 91 -
Rwork0.338 1925 -
all-2016 -
obs--58.91 %

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