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- PDB-4u49: Crystal structure of Pectate Lyase Pel3 from Pectobacterium carot... -

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Basic information

Entry
Database: PDB / ID: 4u49
TitleCrystal structure of Pectate Lyase Pel3 from Pectobacterium carotovorum with two monomers in the A.U
ComponentsPectate lyase
KeywordsLYASE / Protein secretion / bacterial pathogenesis
Function / homology
Function and homology information


pectate lyase / pectate lyase activity / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBallut, L. / Gouet, P. / Shevchik, V.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-BLAN-1531-SECPATH France
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. / Shevchik, 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 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pectate lyase
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4573
Polymers74,4172
Non-polymers401
Water13,908772
1
A: Pectate lyase


Theoretical massNumber of molelcules
Total (without water)37,2091
Polymers37,2091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pectate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2492
Polymers37,2091
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.600, 72.000, 83.700
Angle α, β, γ (deg.)90.00, 101.30, 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Gene: pel-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q47465
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 772 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 33.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Lithium acetate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→35.7 Å / Num. all: 52416 / Num. obs: 52416 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 16.91
Reflection shellResolution: 1.8→10 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.78 / % possible all: 99.8

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Processing

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

3b4n


Resolution: 1.8→35.654 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 2677 5.11 %
Rwork0.1775 --
obs0.1794 52403 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→35.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4706 0 1 772 5479
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034785
X-RAY DIFFRACTIONf_angle_d0.7646461
X-RAY DIFFRACTIONf_dihedral_angle_d10.8361745
X-RAY DIFFRACTIONf_chiral_restr0.028731
X-RAY DIFFRACTIONf_plane_restr0.003850
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7984-1.83110.29931330.25792438X-RAY DIFFRACTION94
1.8311-1.86640.29321290.23832654X-RAY DIFFRACTION100
1.8664-1.90450.2771640.22262546X-RAY DIFFRACTION100
1.9045-1.94590.27421450.21062661X-RAY DIFFRACTION100
1.9459-1.99110.24861400.20232582X-RAY DIFFRACTION100
1.9911-2.04090.23131390.19572624X-RAY DIFFRACTION100
2.0409-2.09610.22411400.18452632X-RAY DIFFRACTION100
2.0961-2.15780.20961330.1852616X-RAY DIFFRACTION100
2.1578-2.22740.22031330.17792659X-RAY DIFFRACTION100
2.2274-2.3070.23011360.18582607X-RAY DIFFRACTION100
2.307-2.39930.2521420.18582617X-RAY DIFFRACTION100
2.3993-2.50850.23651470.19412611X-RAY DIFFRACTION100
2.5085-2.64070.20011250.1882643X-RAY DIFFRACTION100
2.6407-2.80610.23021420.18812626X-RAY DIFFRACTION100
2.8061-3.02270.21161590.18662615X-RAY DIFFRACTION100
3.0227-3.32670.19621490.17082612X-RAY DIFFRACTION100
3.3267-3.80760.19391380.15512653X-RAY DIFFRACTION100
3.8076-4.79530.16851550.14162633X-RAY DIFFRACTION99
4.7953-35.66080.2111280.16942697X-RAY DIFFRACTION99

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