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- PDB-5zu4: Crystal structure of Lamprey immune protein -

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Basic information

Entry
Database: PDB / ID: 5zu4
TitleCrystal structure of Lamprey immune protein
ComponentsNatterin-like protein
KeywordsANTITUMOR PROTEIN / lamprey / pore-forming protein / cytotoxin
Function / homology: / Aerolysin-like toxin / Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / DI(HYDROXYETHYL)ETHER / Natterin-like protein
Function and homology information
Biological speciesLethenteron camtschaticum (Arctic lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsLi, Q.W. / Pang, Y.
CitationJournal: To Be Published
Title: Structure of a pore-forming protein
Authors: Li, Q.W. / Pang, Y.
History
DepositionMay 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2019Provider: 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: Natterin-like protein
B: Natterin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,91921
Polymers68,6822
Non-polymers1,23719
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-17 kcal/mol
Surface area28160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.049, 105.049, 168.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Natterin-like protein


Mass: 34340.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lethenteron camtschaticum (Arctic lamprey)
Production host: Escherichia coli (E. coli) / References: UniProt: K7WEH5

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Non-polymers , 5 types, 157 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 1,4-Dioxane, Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9798 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.25→89.08 Å / Num. obs: 41118 / % possible obs: 99.9 % / Redundancy: 16 % / Net I/σ(I): 28.3
Reflection shellResolution: 2.25→2.29 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NZO

4nzo


Resolution: 2.39→89.08 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.38 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.227
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 1897 5 %RANDOM
Rwork0.1926 ---
obs0.1953 35701 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 164.27 Å2 / Biso mean: 52.299 Å2 / Biso min: 25.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å2-0 Å2-0 Å2
2--0.37 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 2.39→89.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 75 138 5023
Biso mean--67.76 44.58 -
Num. residues----627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194967
X-RAY DIFFRACTIONr_bond_other_d0.0020.024734
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9546682
X-RAY DIFFRACTIONr_angle_other_deg0.947310942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6765629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87324.718195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15815871
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4851518
X-RAY DIFFRACTIONr_chiral_restr0.10.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021083
LS refinement shellResolution: 2.389→2.451 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 137 -
Rwork0.296 2507 -
all-2644 -
obs--96.22 %

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