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- PDB-2iq7: Crystal structure of the polygalacturonase from Colletotrichum lu... -

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Basic information

Entry
Database: PDB / ID: 2iq7
TitleCrystal structure of the polygalacturonase from Colletotrichum lupini and its implications for the interaction with polygalacturonase-inhibiting proteins
Componentsendopolygalacturonase
KeywordsHYDROLASE / parallel beta helix
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
ACETIC ACID / DI(HYDROXYETHYL)ETHER / endo-polygalacturonase
Similarity search - Component
Biological speciesColletotrichum lupini (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsBonivento, D. / Federici, L. / Matteo, A.D.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of the endopolygalacturonase from the phytopathogenic fungus Colletotrichum lupini and its interaction with polygalacturonase-inhibiting proteins
Authors: Bonivento, D. / Pontiggia, D. / Matteo, A.D. / Fernandez-Recio, J. / Salvi, G. / Tsernoglou, D. / Cervone, F. / Lorenzo, G.D. / Federici, L.
History
DepositionOct 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / 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.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT THE UNP ...SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT THE UNP SEQUENCE DATABASE. HOWEVER, THE SEQUENCE HAS BEEN SUBMITTED TO GENEBANK.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: endopolygalacturonase
B: endopolygalacturonase
C: endopolygalacturonase
D: endopolygalacturonase
E: endopolygalacturonase
F: endopolygalacturonase
G: endopolygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,66024
Polymers239,4977
Non-polymers5,16317
Water43,9212438
1
A: endopolygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4813
Polymers34,2141
Non-polymers1,2672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: endopolygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9995
Polymers34,2141
Non-polymers7854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: endopolygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8323
Polymers34,2141
Non-polymers6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: endopolygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8323
Polymers34,2141
Non-polymers6192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: endopolygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9394
Polymers34,2141
Non-polymers7253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: endopolygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9394
Polymers34,2141
Non-polymers7253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: endopolygalacturonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6382
Polymers34,2141
Non-polymers4241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.640, 127.266, 205.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsseven monomers are present in the asymmetric unit, each representing a biological unit

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Components

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Protein , 1 types, 7 molecules ABCDEFG

#1: Protein
endopolygalacturonase


Mass: 34213.848 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Colletotrichum lupini (fungus) / References: UniProt: A1E266, endo-polygalacturonase

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Sugars , 2 types, 7 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 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]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: 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.: 6
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

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Non-polymers , 4 types, 2448 molecules

#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2438 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 24% PEG3000, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.94→105.41 Å / Num. all: 165995 / Num. obs: 165995 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.4
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.396 / Num. unique all: 16003 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CZF

1czf


Resolution: 1.94→49.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.516 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19619 8252 5 %RANDOM
Rwork0.15182 ---
obs0.15407 155991 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.117 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2--0.79 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.94→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16781 0 322 2438 19541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02217602
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.95323965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36352443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.05825.939554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.284152704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7651521
X-RAY DIFFRACTIONr_chiral_restr0.0790.22861
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212846
X-RAY DIFFRACTIONr_nbd_refined0.1980.28360
X-RAY DIFFRACTIONr_nbtor_refined0.3030.211905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.22126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.2172
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.2132
X-RAY DIFFRACTIONr_mcbond_it0.5581.511942
X-RAY DIFFRACTIONr_mcangle_it0.92218784
X-RAY DIFFRACTIONr_scbond_it1.72436422
X-RAY DIFFRACTIONr_scangle_it2.6744.55142
LS refinement shellResolution: 1.94→1.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 580 -
Rwork0.174 11137 -
obs--96.2 %

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