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- PDB-1hg8: Endopolygalacturonase from the phytopathogenic fungus Fusarium mo... -

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Basic information

Entry
Database: PDB / ID: 1hg8
TitleEndopolygalacturonase from the phytopathogenic fungus Fusarium moniliforme
ComponentsENDOPOLYGALACTURONASE
KeywordsHYDROLASE / PECTIN DEGRADATION
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
Biological speciesFUSARIUM MONILIFORME (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.73 Å
AuthorsFederici, L. / Caprari, C. / Mattei, B. / Savino, C. / De Lorenzo, G. / Cervone, F. / Tsernoglou, D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structural Requirements of Endopolygalacturonase for the Interaction with Pgip (Polygalacturonase-Inhibiting Protein)
Authors: Federici, L. / Caprari, C. / Mattei, B. / Savino, C. / Di Matteo, A. / De Lorenzo, G. / Cervone, F. / Tsernoglou, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and Preliminary X-Ray Diffraction Study of the Endo-Polygalacturonase from Fusarium Moniliforme.
Authors: Federici, L. / Mattei, B. / Caprari, C. / Savino, C. / Cervone, F. / Tsernoglou, D.
History
DepositionDec 13, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2001Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
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 / 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 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: ENDOPOLYGALACTURONASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8683
Polymers36,2221
Non-polymers6462
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.260, 61.590, 98.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENDOPOLYGALACTURONASE


Mass: 36222.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FUSARIUM MONILIFORME (fungus) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: Q07181
#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.: 1
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: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 40.9 %
Crystal growpH: 4.7 / Details: pH 4.70
Crystal grow
*PLUS
Temperature: 294 K / Method: vapor diffusion, hanging drop
Details: Federici, L., (2001) Acta Crystallogr.,Sect.D, 55, 1359.
pH: 4.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
237-42 %(w/v)PEG40001reservoir
30.1 Msodium citrate1reservoirpH4.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→17.9 Å / Num. obs: 37710 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 4.56 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Num. measured all: 204193
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.302

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.73→17.9 Å / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.203 -5 %RANDOM
Rwork0.1728 ---
obs-37710 99.4 %-
Refinement stepCycle: LAST / Resolution: 1.73→17.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 42 326 2908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d2.1
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.1728 / Rfactor Rfree: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.195

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