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- PDB-7zbf: Crystal structure of native Iripin-4 serpin from tick Ixodes ricinus -

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Basic information

Entry
Database: PDB / ID: 7zbf
TitleCrystal structure of native Iripin-4 serpin from tick Ixodes ricinus
ComponentsIripin-4 serpin
KeywordsIMMUNOSUPPRESSANT / Ixodes ricinus / Iripin-4 / Crystal / Native conformation / Serpin
Function / homology
Function and homology information


negative regulation of peptidase activity / serine-type endopeptidase inhibitor activity / extracellular space
Similarity search - Function
Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors
Similarity search - Domain/homology
NICKEL (II) ION / Putative salivary serpin
Similarity search - Component
Biological speciesIxodes ricinus (castor bean tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsKascakova, B. / Kuta Smatanova, I. / Chmelar, J. / Prudnikova, T.
Funding supportEuropean Union, Czech Republic, 2items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000441European Union
Grant Agency of the Czech Republic19-14704Y Czech Republic
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Conformational transition of the Ixodes ricinus salivary serpin Iripin-4.
Authors: Kascakova, B. / Kotal, J. / Havlickova, P. / Vopatkova, V. / Prudnikova, T. / Grinkevich, P. / Kuty, M. / Chmelar, J. / Kuta Smatanova, I.
History
DepositionMar 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iripin-4 serpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0472
Polymers41,9891
Non-polymers591
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.932, 78.932, 117.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-401-

NI

21A-669-

HOH

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Components

#1: Protein Iripin-4 serpin / Putative salivary serpin


Mass: 41988.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes ricinus (castor bean tick) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K8RJV9
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25 % w/v Polyethylene glycol 3,350, 100 mM BIS-TRIS, 200 mM Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→44.62 Å / Num. obs: 19373 / % possible obs: 99.7 % / Redundancy: 14.96 % / CC1/2: 0.999 / Rrim(I) all: 0.096 / Net I/σ(I): 22.47
Reflection shellResolution: 2.3→2.44 Å / Mean I/σ(I) obs: 4.3 / Num. unique obs: 3085 / CC1/2: 0.928 / Rrim(I) all: 0.624

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.372
Highest resolutionLowest resolution
Rotation44.62 Å2.52 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3nda

3nda


Resolution: 2.3→44.62 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.685 / SU ML: 0.185 / SU R Cruickshank DPI: 0.3432 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 969 5 %RANDOM
Rwork0.1971 ---
obs0.1999 18404 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.94 Å2 / Biso mean: 39.8 Å2 / Biso min: 4.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0.45 Å2-0 Å2
2---0.9 Å20 Å2
3---2.93 Å2
Refinement stepCycle: final / Resolution: 2.3→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 1 205 3168
Biso mean--33.51 41.48 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133019
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152905
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.6354094
X-RAY DIFFRACTIONr_angle_other_deg1.2471.5766663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.795375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97621.988161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01915518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4961521
X-RAY DIFFRACTIONr_chiral_restr0.060.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023417
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 70 -
Rwork0.234 1340 -
all-1410 -
obs--99.37 %

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