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- PDB-2pec: THE REFINED THREE-DIMENSIONAL STRUCTURE OF PECTATE LYASE C FROM E... -

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Entry
Database: PDB / ID: 2pec
TitleTHE REFINED THREE-DIMENSIONAL STRUCTURE OF PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT 2.2 ANGSTROMS RESOLUTION: IMPLICATIONS FOR AN ENZYMATIC MECHANISM
ComponentsPECTATE LYASE C
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 / 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 speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsYoder, M.D. / Jurnak, F.
Citation
Journal: FASEB J. / Year: 1995
Title: Protein motifs. 3. The parallel beta helix and other coiled folds.
Authors: Yoder, M.D. / Jurnak, F.
#1: Journal: Structure / Year: 1993
Title: Unusual Structural Features of the Parallel Beta-Helix of the Pectate Lyases
Authors: Yoder, M.D. / Lietzke, S.E. / Jurnak, F.
#2: Journal: Science / Year: 1993
Title: New Domain Motif: The Structure of Pectate Lyase C, a Secreted Plant Virulence Factor
Authors: Yoder, M.D. / Keen, N.T. / Jurnak, F.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: Preliminary Crystallographic Analysis of the Plant Pathogenic Factor, Pectate Lyase C from Erwinia Chrysanthemi
Authors: Yoder, M.D. / Dechaine, C.A. / Jurnak, F.
#4: Journal: J.Bacteriol. / Year: 1988
Title: Structure and Organization of the Pel Genes from Erwinia Chrysanthemi Ec16
Authors: Tamaki, S.J. / Gold, S. / Robeson, M. / Manulis, S. / Keen, N.T.
History
DepositionAug 8, 1994Processing site: BNL
SupersessionFeb 14, 1995ID: 1PEC
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 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PECTATE LYASE C


Theoretical massNumber of molelcules
Total (without water)37,7341
Polymers37,7341
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.380, 80.260, 95.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 220
2: THE SIDE-CHAIN DENSITY FOR RESIDUES THR 16, LYS 43, LYS 44, LYS 109, ASN 161, LYS 285, ASN 321, AND LYS 333 IS UNCLEAR AND NOT COMPLETELY RESOLVED.

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Components

#1: Protein PECTATE LYASE C


Mass: 37733.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Gene: PPEL410 OF PELC / References: UniProt: P11073, pectate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.85 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 2
Details: THE SIDE-CHAIN DENSITY FOR RESIDUES THR 16, LYS 43, LYS 44, LYS 109, ASN 161, LYS 285, ASN 321, AND LYS 333 IS UNCLEAR AND NOT COMPLETELY RESOLVED.
RfactorNum. reflection
Rwork0.1797 -
obs0.1797 27769
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 0 114 2763
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.768
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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