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- PDB-7bbv: Pectate lyase B from Verticillium dahliae -

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Basic information

Entry
Database: PDB / ID: 7bbv
TitlePectate lyase B from Verticillium dahliae
ComponentsPectate lyase B
KeywordsLYASE / Pectinase / Beta-sheets
Function / homology
Function and homology information


pectate lyase activity / polysaccharide 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
alpha-D-mannopyranose / DI(HYDROXYETHYL)ETHER / Pectate lyase B
Similarity search - Component
Biological speciesVerticillium dahliae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsSafran, J. / Habrylo, O. / Bouckaert, J. / Pau Roblot, C. / Senechal, F. / Pelloux, J.
Funding supportEuropean Union, France, 2items
OrganizationGrant numberCountry
European Regional Development FundEuropean Union
Agence Nationale de la Recherche (ANR)CARAPEC-Region Hauts de France France
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: The specificity of pectate lyase VdPelB from Verticilium dahliae is highlighted by structural, dynamical and biochemical characterizations.
Authors: Safran, J. / Ung, V. / Bouckaert, J. / Habrylo, O. / Molinie, R. / Fontaine, J.X. / Lemaire, A. / Voxeur, A. / Pilard, S. / Pau-Roblot, C. / Mercadante, D. / Pelloux, J. / Senechal, F.
History
DepositionDec 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)75,90417
Polymers73,5562
Non-polymers2,34815
Water18,9341051
1
A: Pectate lyase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8998
Polymers36,7781
Non-polymers1,1217
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Pectate lyase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0059
Polymers36,7781
Non-polymers1,2278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.890, 59.690, 93.870
Angle α, β, γ (deg.)90.000, 96.350, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 19 through 23 or resid 25...
d_2ens_1(chain "B" and (resid 19 through 23 or resid 25...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAGLUA1 - 5
d_12ens_1CYSVALA9 - 61
d_13ens_1VALSERA63 - 75
d_14ens_1LEUVALA78 - 88
d_15ens_1ASNSERA91 - 197
d_16ens_1ARGGLYA199 - 214
d_17ens_1SERTHRA216 - 237
d_18ens_1ASNASPA240 - 246
d_19ens_1LYSALAA250 - 255
d_110ens_1VALGLYA259 - 277
d_111ens_1SERTYRA281 - 285
d_112ens_1TYRTYRA288
d_113ens_1LEUPHEA292 - 312
d_114ens_1MANMANB
d_115ens_1MANMANC
d_116ens_1MANMAND
d_117ens_1MANMANE
d_118ens_1MANMANF
d_119ens_1MANMANG
d_21ens_1ALAGLUJ1 - 5
d_22ens_1CYSVALJ9 - 61
d_23ens_1VALSERJ64 - 76
d_24ens_1LEUVALJ78 - 88
d_25ens_1ASNSERJ90 - 196
d_26ens_1ARGARGJ199
d_27ens_1PHEGLYJ202 - 216
d_28ens_1SERTHRJ220 - 241
d_29ens_1ASNASPJ243 - 249
d_210ens_1LYSALAJ253 - 258
d_211ens_1VALGLYJ262 - 280
d_212ens_1SERTYRJ282 - 286
d_213ens_1TYRTYRJ290
d_214ens_1LEUPHEJ293 - 313
d_215ens_1MANMANK
d_216ens_1MANMANL
d_217ens_1MANMANM
d_218ens_1MANMANN
d_219ens_1MANMANO
d_220ens_1MANMANP

NCS oper: (Code: givenMatrix: (0.489434907135, -0.871308290348, -0.0357118306576), (0.869118235362, 0.484036532212, 0.101696255808), (-0.0713229601126, -0.0808115007601, 0.994174298957)Vector: -40. ...NCS oper: (Code: given
Matrix: (0.489434907135, -0.871308290348, -0.0357118306576), (0.869118235362, 0.484036532212, 0.101696255808), (-0.0713229601126, -0.0808115007601, 0.994174298957)
Vector: -40.8319464065, -18.9200123649, -4.23547513539)

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Components

#1: Protein Pectate lyase B


Mass: 36777.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Verticillium dahliae (strain VdLs.17 / ATCC MYA-4575 / FGSC 10137) (fungus)
Strain: VdLs.17 / ATCC MYA-4575 / FGSC 10137 / Gene: VDAG_04718 / Production host: Komagataella pastoris (fungus) / References: UniProt: G2X3Y1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1051 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M MIB 8.0 25 % w/v PEG 1500 (B5 condition PACT premier plate)

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Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→60.52 Å / Num. obs: 207729 / % possible obs: 98.98 % / Redundancy: 2 % / Biso Wilson estimate: 23.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.014 / Rrim(I) all: 0.02 / Net I/σ(I): 18.3
Reflection shellResolution: 1.2→1.24 Å / Num. unique obs: 19578 / CC1/2: 0.136 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
pointlessdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VMV

3vmv


Resolution: 1.2→60.52 Å / SU ML: 0.356 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.8724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1958 10374 5 %
Rwork0.1722 197008 -
obs0.1734 207382 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.19 Å2
Refinement stepCycle: LAST / Resolution: 1.2→60.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4480 0 141 1052 5673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01324798
X-RAY DIFFRACTIONf_angle_d1.39986510
X-RAY DIFFRACTIONf_chiral_restr0.1014765
X-RAY DIFFRACTIONf_plane_restr0.0092810
X-RAY DIFFRACTIONf_dihedral_angle_d13.40361796
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.75524096286 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.46132900.45855464X-RAY DIFFRACTION83.16
1.21-1.230.44353360.44476354X-RAY DIFFRACTION96.37
1.23-1.240.4293440.43436521X-RAY DIFFRACTION98.07
1.24-1.260.43783420.42386495X-RAY DIFFRACTION98.73
1.26-1.270.40933430.42126517X-RAY DIFFRACTION98.71
1.27-1.290.43033450.42026564X-RAY DIFFRACTION98.83
1.29-1.310.42973460.42326562X-RAY DIFFRACTION99.55
1.31-1.330.43663450.42446563X-RAY DIFFRACTION99.45
1.33-1.350.41513460.40046574X-RAY DIFFRACTION99.45
1.35-1.370.39843470.37496575X-RAY DIFFRACTION99.34
1.37-1.40.40083470.36196583X-RAY DIFFRACTION99.21
1.4-1.420.35213460.35136567X-RAY DIFFRACTION99.4
1.42-1.450.36893470.34966586X-RAY DIFFRACTION99.58
1.45-1.480.35593460.34066569X-RAY DIFFRACTION99.37
1.48-1.510.33513460.32096578X-RAY DIFFRACTION99.7
1.51-1.540.31093490.31896619X-RAY DIFFRACTION99.84
1.54-1.580.34173490.31036634X-RAY DIFFRACTION99.8
1.58-1.630.31373470.30096624X-RAY DIFFRACTION99.96
1.63-1.670.29693500.26386653X-RAY DIFFRACTION99.93
1.67-1.730.27883460.23236579X-RAY DIFFRACTION99.97
1.73-1.790.20893500.186665X-RAY DIFFRACTION100
1.79-1.860.20063500.16046644X-RAY DIFFRACTION99.96
1.86-1.950.18583490.1636623X-RAY DIFFRACTION99.97
1.95-2.050.19913500.16516647X-RAY DIFFRACTION100
2.05-2.180.18923510.15736677X-RAY DIFFRACTION100
2.18-2.340.16983510.14696670X-RAY DIFFRACTION100
2.35-2.580.16483510.14326668X-RAY DIFFRACTION100
2.58-2.950.14663510.13336678X-RAY DIFFRACTION99.99
2.95-3.720.15083540.12696728X-RAY DIFFRACTION100
3.72-60.520.16063600.13436827X-RAY DIFFRACTION99.85

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