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- PDB-1kcc: Endopolygalacturonase I from Stereum purpureum complexed with a g... -

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Basic information

Entry
Database: PDB / ID: 1kcc
TitleEndopolygalacturonase I from Stereum purpureum complexed with a galacturonate at 1.00 A resolution.
ComponentsENDOPOLYGALACTURONASE
KeywordsHYDROLASE / BETA HELICAL STRUCTURE / GLYCOSIDE HYDROLASE / SILVER-LEAF INDUCING SUBSTANCE
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
beta-D-galactopyranuronic acid / endo-polygalacturonase
Similarity search - Component
Biological speciesChondrostereum purpureum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsShimizu, T. / Nakatsu, T. / Miyairi, K. / Okuno, T. / Kato, H.
Citation
Journal: Biochemistry / Year: 2002
Title: Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution.
Authors: Shimizu, T. / Nakatsu, T. / Miyairi, K. / Okuno, T. / Kato, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray study of endopolygalacturonase from the pathogenic fungus Stereum purpureum
Authors: Shimizu, T. / Nakatsu, T. / Miyairi, K. / Okuno, T. / Kato, H.
#2: Journal: Eur.J.Biochem. / Year: 2000
Title: Determination of glycosylation sites, disulfide bridges, and the C-terminus of Stereum purpureum mature endopolygalacturonase I by electrospray ionization mass spectrometry
Authors: Shimizu, T. / Miyairi, K. / Okuno, T.
#3: Journal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 1998
Title: Isolation, characterization, and sugar chain structure of endoPG Ia, Ib and Ic from Stereum purpureum
Authors: Hasui, Y. / Fukui, Y. / Kikuchi, J. / Kato, N. / Miyairi, K. / Okuno, T.
History
DepositionNov 8, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 5, 2002Provider: 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 14, 2015Group: Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOPOLYGALACTURONASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3476
Polymers34,6521
Non-polymers6955
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.515, 52.138, 37.187
Angle α, β, γ (deg.)72.31, 69.09, 70.35
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ENDOPOLYGALACTURONASE


Mass: 34652.363 Da / Num. of mol.: 1 / Fragment: residues 1-335 / Source method: isolated from a natural source / Source: (natural) Chondrostereum purpureum (fungus) / Strain: ASP-4B / References: UniProt: P79074, endo-polygalacturonase

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Sugars , 2 types, 3 molecules

#2: Sugar ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H10O7
IdentifierTypeProgram
DGalpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#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.: 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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Non-polymers , 3 types, 587 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 1.65 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Shimizu, T., (2001) Acta Crystallogr., Sect.D, 57, 1171.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium acetate1droppH5.0
210 mg/mlprotein1drop
350 mMsodium acetate1reservoirpH5.0
40.2 M1reservoirNaCl
512-17.5 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1→25.3 Å / Num. all: 152404 / Num. obs: 152404 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 6.38 Å2 / Rsym value: 0.053 / Net I/σ(I): 6.1
Reflection shellResolution: 1→1.05 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.172 / % possible all: 89.9
Reflection
*PLUS
Num. measured all: 649682 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 89.9 % / Rmerge(I) obs: 0.172

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K5C

1k5c


Resolution: 1→10 Å / Num. parameters: 27865 / Num. restraintsaints: 33653 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1364 7627 5.3 %RANDOM
Rwork0.1094 ---
obs0.114 152299 89.1 %-
all-144672 --
Refine analyzeNum. disordered residues: 20 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2982.98
Refinement stepCycle: LAST / Resolution: 1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 43 585 3043
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0343
X-RAY DIFFRACTIONs_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.092
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor all: 0.114 / Rfactor obs: 0.109 / Rfactor Rfree: 0.134 / Rfactor Rwork: 0.109
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.034
X-RAY DIFFRACTIONs_chiral_restr0.101

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