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- PDB-5x2i: Polygalacturonate Lyase by Fusing with a Self-assembling Amphipat... -

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Basic information

Entry
Database: PDB / ID: 5x2i
TitlePolygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide
ComponentsPectate lyase
KeywordsLYASE / tag-fusion enzyme / protein stability / hydrophobic force
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 speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsZhao, W.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31401638 China
CitationJournal: To be published
Title: Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide
Authors: Zhao, W.X.
History
DepositionJan 31, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5213
Polymers43,4451
Non-polymers762
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-20 kcal/mol
Surface area15090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.094, 51.212, 51.296
Angle α, β, γ (deg.)67.51, 74.93, 78.75
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Pectate lyase / Polygalacturonate Lyase / PL


Mass: 43445.191 Da / Num. of mol.: 1 / Fragment: UNP residues 22-420
Source method: isolated from a genetically manipulated source
Details: AEAEAKAKAEAEAKAK was the Self-assembling Amphipathic PeptideWISPTPPTTPTPPTTPTPTPAMD was the linker peptide.
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: pel, BSU07560 / Production host: Escherichia coli (E. coli) / References: UniProt: P39116, pectate lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 0.2 M sodium bromide, 20 mM Glycine-NaOH, 20 % polyethylene glycol 3350, 7 mM calcium chloride, 20 % glycerol
PH range: 7.2-7.8

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→28.427 Å / Num. obs: 18202 / % possible obs: 91.8 % / Redundancy: 2.3 % / Net I/σ(I): 12.1

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Processing

SoftwareName: REFMAC / Version: 5.8.0135 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1BN8

1bn8


Resolution: 2.05→28.427 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.411 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.187 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19952 1051 5.5 %RANDOM
Rwork0.17581 ---
obs0.17709 18202 83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.746 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20.39 Å20.31 Å2
2---0.26 Å2-0.73 Å2
3---1.19 Å2
Refinement stepCycle: 1 / Resolution: 2.05→28.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3066 0 2 169 3237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193137
X-RAY DIFFRACTIONr_bond_other_d0.0060.022807
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9234261
X-RAY DIFFRACTIONr_angle_other_deg0.95436470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2915398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.69425.133150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08715491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2471511
X-RAY DIFFRACTIONr_chiral_restr0.1170.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9612.2461595
X-RAY DIFFRACTIONr_mcbond_other1.9612.2431594
X-RAY DIFFRACTIONr_mcangle_it2.6773.3551992
X-RAY DIFFRACTIONr_mcangle_other2.6773.3591993
X-RAY DIFFRACTIONr_scbond_it2.6612.4241542
X-RAY DIFFRACTIONr_scbond_other2.6592.4241542
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8183.5352269
X-RAY DIFFRACTIONr_long_range_B_refined5.26818.4013629
X-RAY DIFFRACTIONr_long_range_B_other5.19818.2473593
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.182 40 -
Rwork0.186 705 -
obs--43.82 %

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