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- PDB-1k5c: Endopolygalacturonase I from Stereum purpureum at 0.96 A resolution -

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Basic information

Entry
Database: PDB / ID: 1k5c
TitleEndopolygalacturonase I from Stereum purpureum at 0.96 A resolution
ComponentsENDOPOLYGALACTURONASEPolygalacturonase
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 / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
endo-polygalacturonase
Similarity search - Component
Biological speciesChondrostereum purpureum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.96 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
DepositionOct 10, 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._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

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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)35,3146
Polymers34,6521
Non-polymers6625
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.396, 52.023, 37.344
Angle α, β, γ (deg.)72.50, 68.93, 69.24
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ENDOPOLYGALACTURONASE / Polygalacturonase


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
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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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: 1.61 Å3/Da / Density % sol: 44.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Dec 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 0.96→41.5 Å / Num. all: 171534 / Num. obs: 171534 / % possible obs: 94 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 11.2 Å2 / Rsym value: 0.037 / Net I/σ(I): 5.6
Reflection shellResolution: 0.96→1.01 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.206 / % possible all: 89.4
Reflection
*PLUS
Num. measured all: 1186116 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 89.4 % / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 0.96→10 Å / Num. parameters: 27168 / Num. restraintsaints: 32409 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1398 8572 5.3 %RANDOM
Rwork0.1137 ---
all0.1137 171380 --
obs0.115 162808 90 %-
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2897.1
Refinement stepCycle: LAST / Resolution: 0.96→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 41 504 2964
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0344
X-RAY DIFFRACTIONs_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.114
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_adps0.091
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor all: 0.114 / Rfactor Rfree: 0.14 / Rfactor Rwork: 0.114
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0189
X-RAY DIFFRACTIONs_plane_restr0.034
X-RAY DIFFRACTIONs_chiral_restr0.117

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