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- PDB-4u4b: Crystal Structure of Pectate Lyase Pel3 from Pectobacterium carot... -

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Basic information

Entry
Database: PDB / ID: 4u4b
TitleCrystal Structure of Pectate Lyase Pel3 from Pectobacterium carotovorum with one monomer in the A.U.
ComponentsPectate lyase
KeywordsLYASE / Protein secretion / bacterial pathogenesis
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding
Similarity search - Function
Pectate lyase PlyH/PlyE-like / Pectate lyase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...Pectate lyase PlyH/PlyE-like / Pectate lyase / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBallut, L. / Gouet, P. / Shevchik, V.E.
CitationJournal: To Be Published
Title: Crystal Structure of Pectate Lyase Pel3 from Pectobacterium carotovorum with one monomer in the A.U.
Authors: Ballut, L. / Gouet, P. / Schevchik, V.E. / Pineau, C. / Guschinskaya, N.
History
DepositionJul 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3673
Polymers37,2091
Non-polymers1582
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-8 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.000, 44.350, 86.250
Angle α, β, γ (deg.)90.00, 93.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Pectate lyase


Mass: 37208.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Gene: pel-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C41 / References: UniProt: Q47465
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.92 Å3/Da / Density % sol: 35.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M succinic acid, 0.1M HEPES, 1% (m/v) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.939 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.1→19.7 Å / Num. all: 15124 / Num. obs: 15124 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.87 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 19.17
Reflection shellResolution: 2.1→9.39 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 6.71 / % possible all: 60.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B4N

3b4n


Resolution: 2.1→19.7 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 757 5.01 %
Rwork0.1703 --
obs0.1743 15116 91.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 9 183 2630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082489
X-RAY DIFFRACTIONf_angle_d1.1163362
X-RAY DIFFRACTIONf_dihedral_angle_d14.036914
X-RAY DIFFRACTIONf_chiral_restr0.041378
X-RAY DIFFRACTIONf_plane_restr0.005442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.26210.32351110.20382091X-RAY DIFFRACTION68
2.2621-2.48940.26821580.19093016X-RAY DIFFRACTION96
2.4894-2.84860.27271610.18043045X-RAY DIFFRACTION98
2.8486-3.58550.25631620.16213078X-RAY DIFFRACTION99
3.5855-19.71340.21031650.15553129X-RAY DIFFRACTION97

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