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- PDB-1pcl: UNUSUAL STRUCTURAL FEATURES IN THE PARALLEL BETA-HELIX IN PECTATE... -

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Basic information

Entry
Database: PDB / ID: 1pcl
TitleUNUSUAL STRUCTURAL FEATURES IN THE PARALLEL BETA-HELIX IN PECTATE LYASES
ComponentsPECTATE LYASE E
KeywordsLYASE (ACTING ON POLYSACCHARIDES)
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding
Similarity search - Function
Pectate lyase / Pectin lyase family / Pectate lyase / Amb_all / Pectin lyase fold / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsLietzke, S.E. / Keen, N.T. / Jurnak, F.
Citation
Journal: Structure / Year: 1993
Title: Unusual structural features in the parallel beta-helix in pectate lyases.
Authors: Yoder, M.D. / Lietzke, S.E. / Jurnak, F.
#1: Journal: Plant Physiol. / Year: 1996
Title: The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia Chrysanthemi at 2.2 A Resolution.
Authors: Lietzke, S.E. / Keen, N.T. / Jurnak, F.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Preliminary Crystallographic Analysis of a Plant Pathogenic Factor: Pectate Lyase
Authors: Kim, C.-Y. / Mosser, V. / Keen, N. / Jurnak, F.
#3: Journal: J.Bacteriol. / Year: 1986
Title: Structure of Two Pectate Lyase Genes from Erwinia Chrysanthemi Ec16 and Their High-Level Expression in Escherichia Coli
Authors: Keen, N.T. / Tamaki, S.
History
DepositionNov 5, 1993Processing site: BNL
Revision 1.0Feb 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PECTATE LYASE E


Theoretical massNumber of molelcules
Total (without water)38,2161
Polymers38,2161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.790, 91.140, 102.990
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 PECTATE LYASE E / Coordinate model: Cα atoms only


Mass: 38216.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Gene: PPEL748 OF PELC / References: UniProt: P04960, pectate lyase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.36 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.206 -
obs0.206 16846
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms355 0 0 0 355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.56
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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