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- PDB-1plu: PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI WITH 1 LU+3 ION IN THE ... -

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Basic information

Entry
Database: PDB / ID: 1plu
TitlePECTATE LYASE C FROM ERWINIA CHRYSANTHEMI WITH 1 LU+3 ION IN THE PUTATIVE CALCIUM BINDING SITE
ComponentsPROTEIN (PECTATE LYASE C)
KeywordsLYASE / PECTATE CLEAVAGE / PECTINOLYTIC ACTIVITY / TRANS-ELIMINATION / PARALLEL BETA-HELIX
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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYoder, M.D. / Jurnak, F.A.
CitationJournal: Plant Physiol. / Year: 1995
Title: The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).
Authors: Yoder, M.D. / Jurnak, F.
History
DepositionJun 4, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 13, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PECTATE LYASE C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9092
Polymers37,7341
Non-polymers1751
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.600, 80.600, 95.700
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 PROTEIN (PECTATE LYASE C) / PELC


Mass: 37733.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Erwinia chrysanthemi (bacteria) / Genus: Dickeya / Cellular location: EXTRACELLULAR / Plasmid: HB101 / Strain: EC16 / References: UniProt: P11073, pectate lyase
#2: Chemical ChemComp-LU / LUTETIUM (III) ION / LU


Mass: 174.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Lu
Sequence detailsSEQ. IN SWISS-PROT IS PRECURSOR. C-TERM LYS WAS DISORDERED.

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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: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growpH: 6.9
Details: PROTEIN WAS CRYSTALLIZED FROM 1.0MM LUCL3, 1.0M AMMONIUM SULFATE, AND 50MM HEPES, PH 6.9
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 A280/mlprotein1drop
21.0 M1drop(NH4)2SO4
350 mMHEPES1drop
41 mM1dropLuCl3
52.0 M1reservoir(NH4)2SO4
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jun 1, 1992 / Details: COLLIMATOR
RadiationMonochromator: GRAPHIC CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 24983 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
SDMSSOFTWAREdata collection
SDMSSOFTWAREdata reduction
X-PLORmodel building
X-PLOR3.1refinement
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUS PELC MODEL

Resolution: 2.2→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2 /
RfactorNum. reflection
Rwork0.221 -
obs0.221 24983
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 1 0 2650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.598
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_d1.19
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19

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