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- PDB-1ia5: POLYGALACTURONASE FROM ASPERGILLUS ACULEATUS -

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Basic information

Entry
Database: PDB / ID: 1ia5
TitlePOLYGALACTURONASE FROM ASPERGILLUS ACULEATUS
ComponentsPOLYGALACTURONASE
KeywordsHYDROLASE / POLYGALACTURONASE / GLYCOSYLHYDROLASE
Function / homology
Function and homology information


endo-polygalacturonase / polygalacturonase activity / pectin catabolic process / cell wall organization / extracellular region
Similarity search - Function
: / Polygalacturonase active site. / Glycoside hydrolase, family 28 / Glycosyl hydrolases family 28 / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor ...: / Polygalacturonase active site. / Glycoside hydrolase, family 28 / Glycosyl hydrolases family 28 / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / : / Endopolygalacturonase I
Similarity search - Component
Biological speciesAspergillus aculeatus (mold)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2 Å
AuthorsCho, S.W. / Lee, S. / Shin, W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex.
Authors: Cho, S.W. / Lee, S. / Shin, W.
History
DepositionMar 22, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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: POLYGALACTURONASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,06412
Polymers34,6761
Non-polymers2,38811
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.480, 86.630, 37.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein POLYGALACTURONASE


Mass: 34675.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus aculeatus (mold)
References: GenBank: 3220207, UniProt: O74213*PLUS, endo-polygalacturonase
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 45% 1,6-HEXANEDIOL, 0.1M TRIS-HCL , 0.2M AMMONIUM ACETATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
145 %(v/v)1,6-hexanediol11
20.1 MTris-HCl11
30.2 Mammonium acetate11
410 mg/mlprotein12

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: AREA DETECTOR / Date: Oct 21, 1999 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 52967 / Num. obs: 23026 / % possible obs: 85.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 2.3 % / Biso Wilson estimate: 3.3 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.13 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.124 / % possible all: 81.8
Reflection
*PLUS
Highest resolution: 2.02 Å / Lowest resolution: 25 Å / % possible obs: 90.3 % / Num. measured all: 52967
Reflection shell
*PLUS
% possible obs: 72.1 % / Rmerge(I) obs: 0.132

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Processing

Software
NameVersionClassification
MADNESSdata collection
SCALAdata scaling
SHARPphasing
CNSrefinement
MADNESSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2→44.74 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1060 4.99 %RANDOM
Rwork0.171 ---
all0.165 21242 --
obs0.165 21242 --
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→44.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 149 193 2775
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_mcangle_it2.36
X-RAY DIFFRACTIONc_mcbond_it1.82
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.267 172 -
Rwork0.202 --
obs-2976 81.8 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor Rfree: 0.213 / Highest resolution: 2.02 Å / Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_mcbond_it1.82
X-RAY DIFFRACTIONc_mcangle_it2.36
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.202

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