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- PDB-7zas: Crystal structure of cleaved Iripin-4 serpin from tick Ixodes ricinus -

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Basic information

Entry
Database: PDB / ID: 7zas
TitleCrystal structure of cleaved Iripin-4 serpin from tick Ixodes ricinus
Components(Iripin-4 serpin) x 2
KeywordsIMMUNOSUPPRESSANT / Ixodes ricinus / Iripin-4 / Crystal / Cleaved 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
Putative salivary serpin
Similarity search - Component
Biological speciesIxodes ricinus (castor bean tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2May 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 1.3May 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 1.4May 1, 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

Downloads & links

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Assembly

Deposited unit
A: Iripin-4 serpin
aa: Iripin-4 serpin
B: Iripin-4 serpin
bb: Iripin-4 serpin
C: Iripin-4 serpin
cc: Iripin-4 serpin
D: Iripin-4 serpin
dd: Iripin-4 serpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,16912
Polymers168,0278
Non-polymers1424
Water22,9871276
1
A: Iripin-4 serpin
aa: Iripin-4 serpin
D: Iripin-4 serpin
dd: Iripin-4 serpin
hetero molecules


  • defined by author&software
  • Evidence: Analysis of protein interfaces by PDBePISA suggests that the following quaternary structures form assemblies between A-D and B-C chains.
  • 84.1 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)84,0846
Polymers84,0144
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-88 kcal/mol
Surface area27740 Å2
MethodPISA
2
B: Iripin-4 serpin
bb: Iripin-4 serpin
hetero molecules

C: Iripin-4 serpin
cc: Iripin-4 serpin
hetero molecules


  • defined by author&software
  • 84.1 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)84,0846
Polymers84,0144
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area12120 Å2
ΔGint-89 kcal/mol
Surface area28090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.699, 138.414, 80.217
Angle α, β, γ (deg.)90.000, 107.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37855.051 Da / Num. of mol.: 4
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: Protein/peptide
Iripin-4 serpin / Putative salivary serpin


Mass: 4151.742 Da / Num. of mol.: 4
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
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 1276 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Ammonium acetate, 0.1 M BIS-Tris, 25 % w/v PEG 3350

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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 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→46.42 Å / Num. obs: 91690 / % possible obs: 99.3 % / Redundancy: 6.92 % / Biso Wilson estimate: 33.66 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.167 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.12 Å / Num. unique obs: 14692 / CC1/2: 0.773 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.512
Highest resolutionLowest resolution
Rotation46.13 Å2.64 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: MrBUMP

Resolution: 2→46.42 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.983 / SU ML: 0.16 / SU R Cruickshank DPI: 0.2259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 2100 2.3 %RANDOM
Rwork0.187 ---
obs0.1884 89590 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.4 Å2 / Biso mean: 26.222 Å2 / Biso min: 3.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20 Å2-0.44 Å2
2--0.03 Å20 Å2
3---1.61 Å2
Refinement stepCycle: final / Resolution: 2→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11786 0 4 1323 13113
Biso mean--39.23 33.56 -
Num. residues----1495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01312110
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511645
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.63516443
X-RAY DIFFRACTIONr_angle_other_deg1.2621.57726738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.91451521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9322.074651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.356152083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0861584
X-RAY DIFFRACTIONr_chiral_restr0.0610.21628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213745
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022827
LS refinement shellResolution: 2→2.049 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.299 151 -
Rwork0.268 6461 -
obs--97.18 %

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