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- PDB-1bhe: POLYGALACTURONASE FROM ERWINIA CAROTOVORA SSP. CAROTOVORA -

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Basic information

Entry
Database: PDB / ID: 1bhe
TitlePOLYGALACTURONASE FROM ERWINIA CAROTOVORA SSP. CAROTOVORA
ComponentsPOLYGALACTURONASE
KeywordsGLYCOSIDASE / FAMILY 28 GLYCOSYL HYDROLASE / HYDROLYSES POLYGALACTURONIC ACID
Function / homology
Function and homology information


endo-polygalacturonase / polygalacturonase activity / cell wall organization / carbohydrate metabolic process / extracellular region
Similarity search - Function
: / Polygalacturonase active site. / Glycoside hydrolase, family 28 / Glycosyl hydrolases family 28 / 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 speciesPectobacterium carotovorum subsp. carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsPickersgill, R. / Smith, D. / Worboys, K. / Jenkins, J.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora.
Authors: Pickersgill, R. / Smith, D. / Worboys, K. / Jenkins, J.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYGALACTURONASE


Theoretical massNumber of molelcules
Total (without water)40,1351
Polymers40,1351
Non-polymers00
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.229, 53.033, 103.093
Angle α, β, γ (deg.)90.00, 112.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein POLYGALACTURONASE / PEHA


Mass: 40135.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum subsp. carotovorum (bacteria)
Species: Pectobacterium carotovorum / Strain: subsp. carotovorum
Description: SEE H. HEMILA, R. PAKKANEN, R. HEIKINHEIMO, E. TAPIO PALVA & I. PALVA (1992) GENE 116, 27-33
Production host: Bacillus subtilis (bacteria) / References: UniProt: P26509, endo-polygalacturonase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.7 Å3/Da / Density % sol: 42 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG 8000, 0.1M SODIUM CACODYLATE, PH 6.5, 0.2M MAGNESIUM ACETATE.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG60001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoir
45 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 31103 / % possible obs: 97 % / Redundancy: 3 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 21
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 9 / % possible all: 95
Reflection shell
*PLUS
% possible obs: 95.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→12.5 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE DENSITY AND STEREOCHEMISTRY FOR ASP 129 ARE POOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1567 5 %RANDOM
Rwork0.198 ---
obs-30997 96 %-
Displacement parametersBiso mean: 16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2813 0 0 295 3108
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0050.02
X-RAY DIFFRACTIONp_angle_d0.0210.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0190.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6962
X-RAY DIFFRACTIONp_mcangle_it1.1373
X-RAY DIFFRACTIONp_scbond_it0.8292
X-RAY DIFFRACTIONp_scangle_it1.3523
X-RAY DIFFRACTIONp_plane_restr0.0170.03
X-RAY DIFFRACTIONp_chiral_restr0.0710.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.220.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1930.3
X-RAY DIFFRACTIONp_planar_tor3.47
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor4320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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