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- PDB-7qtz: Crystal structure of Iripin-1 serpin from tick Ixodes ricinus -

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Basic information

Entry
Database: PDB / ID: 7qtz
TitleCrystal structure of Iripin-1 serpin from tick Ixodes ricinus
ComponentsPutative salivary serpin
KeywordsIMMUNOSUPPRESSANT / Ixodes ricinus / Iripin-1 / Crystal / HYDROLASE
Function / homology
Function and homology information


immune system process / 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
Biological speciesIxodes ricinus (castor bean tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsKascakova, B. / Kuta Smatanova, I. / Chmelar, J. / Prudnikova, T.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/15_003/0000441 Czech Republic
Grant Agency of the Czech Republic19-14704Y Czech Republic
The Grant Agency of The University of South Bohemia105/2019/P Czech Republic
CitationJournal: Front Immunol / Year: 2023
Title: Iripin-1, a new anti-inflammatory tick serpin, inhibits leukocyte recruitment in vivo while altering the levels of chemokines and adhesion molecules.
Authors: Chlastakova, A. / Kascakova, B. / Kotal, J. / Langhansova, H. / Kotsyfakis, M. / Kuta Smatanova, I. / Tirloni, L. / Chmelar, J.
History
DepositionJan 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 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: Putative salivary serpin
B: Putative salivary serpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6813
Polymers84,6572
Non-polymers241
Water9,026501
1
A: Putative salivary serpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3532
Polymers42,3291
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative salivary serpin


Theoretical massNumber of molelcules
Total (without water)42,3291
Polymers42,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.819, 91.005, 95.833
Angle α, β, γ (deg.)90.000, 97.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative salivary serpin / Serpin-1


Mass: 42328.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes ricinus (castor bean tick) / Production host: Escherichia coli (E. coli) / References: UniProt: Q06B75
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Nickel(II) sufate hexahydrate, Hepes, Jeffamine M-600

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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 2M / Detector: PIXEL / Date: Apr 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.097→95.006 Å / Num. all: 48379 / Num. obs: 48379 / % possible obs: 99.2 % / Redundancy: 6.8 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.144 / Rsym value: 0.133 / Net I/av σ(I): 5.5 / Net I/σ(I): 10.7 / Num. measured all: 331161
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.216.81.090.74754969530.4461.1791.091.797.7
2.21-2.346.50.75514320466250.3160.820.7552.498.7
2.34-2.517.10.5471.44488262800.2190.590.5473.499.9
2.51-2.717.10.3722.14155658850.150.4010.3724.999.9
2.71-2.976.80.2373.23655353700.0980.2570.2377.599.5
2.97-3.326.90.1335.73370148920.0550.1450.13312.799.4
3.32-3.8370.0799.33046543280.0330.0860.07920.699.9
3.83-4.696.50.05512.42338036240.0240.060.05527.699.1
4.69-6.636.90.04913.51971828380.020.0540.04930.599.6
6.63-48.3986.40.03416.71015315840.0150.0370.03439.499

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.526
Highest resolutionLowest resolution
Rotation48.4 Å2.29 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3nda

3nda


Resolution: 2.1→48.44 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.465 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 2464 5.1 %RANDOM
Rwork0.1902 ---
obs0.1933 45891 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.44 Å2 / Biso mean: 38.591 Å2 / Biso min: 13.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20.74 Å2
2--2.07 Å20 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 2.1→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5629 0 1 521 6151
Biso mean--21.83 42.27 -
Num. residues----710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135791
X-RAY DIFFRACTIONr_bond_other_d0.0020.0155479
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.6357847
X-RAY DIFFRACTIONr_angle_other_deg1.3011.58312557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6695716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08122.883326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23215977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1281535
X-RAY DIFFRACTIONr_chiral_restr0.0640.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021434
LS refinement shellResolution: 2.1→2.151 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.316 183 -
Rwork0.271 3258 -
obs--95.72 %

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