[English] 日本語
Yorodumi
- PDB-7ahp: Crystal structure of Ixodes ricinus serpin - Iripin-3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ahp
TitleCrystal structure of Ixodes ricinus serpin - Iripin-3
Components(Putative salivary serpin) x 2
KeywordsHYDROLASE INHIBITOR / Serpin / Inhibitor / Ixodes ricinus / HYDROLASE
Function / homology
Function and homology information


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
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Putative salivary serpin
Similarity search - Component
Biological speciesIxodes ricinus (castor bean tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKascakova, B. / Kuta Smatanova, I. / Prudnikova, T.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic19-14704Y Czech Republic
CitationJournal: Front Immunol / Year: 2021
Title: Iripin-3, a New Salivary Protein Isolated From Ixodes ricinus Ticks, Displays Immunomodulatory and Anti-Hemostatic Properties In Vitro
Authors: Chlastakova, A. / Kotal, J. / Berankova, Z. / Kascakova, B. / Martins, L.A. / Langhansova, H. / Prudnikova, T. / Ederova, M. / Kotsyfakis, M. / Chmelar, J.
History
DepositionSep 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative salivary serpin
aa: Putative salivary serpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2365
Polymers42,8702
Non-polymers3663
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-20 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.940, 132.940, 88.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-595-

HOH

31A-695-

HOH

41A-698-

HOH

-
Components

#1: Protein Putative salivary serpin


Mass: 39157.332 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 (E. coli) / References: UniProt: A0A0K8RCY5
#2: Protein/peptide Putative salivary serpin


Mass: 3712.242 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 (E. coli) / References: UniProt: A0A0K8RCY5
#3: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTwo protein chains result from protease cleavage (between residues 355 and 363) that is common for ...Two protein chains result from protease cleavage (between residues 355 and 363) that is common for serpins. After binding of the serpin reactive center loop (RCL) to protease and subsequent cleavage and insertion of RCL into beta-sheet A. Chain A corresponds to the N-terminal region generated by the proteolytic event and chain lowercase aa corresponds to the C-terminal region.
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: potassium thiocyanate, sodium cacodylate, PGA

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.95→48.32 Å / Num. obs: 34278 / % possible obs: 99.9 % / Redundancy: 1.573 % / CC1/2: 0.998 / Net I/σ(I): 0.1345
Reflection shellResolution: 1.95→2.07 Å / Num. unique obs: 889221 / CC1/2: 0.826

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3nda

3nda


Resolution: 1.95→48.32 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 1714 5 %RANDOM
Rwork0.1916 ---
obs0.1931 32559 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.72 Å2 / Biso mean: 24.264 Å2 / Biso min: 8.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----1.01 Å2
Refinement stepCycle: final / Resolution: 1.95→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 24 251 3149
Biso mean--59.36 33.37 -
Num. residues----367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132957
X-RAY DIFFRACTIONr_bond_other_d0.0350.0172766
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.6474001
X-RAY DIFFRACTIONr_angle_other_deg2.3071.5746400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.44322.438160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26815501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4071520
X-RAY DIFFRACTIONr_chiral_restr0.1220.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023322
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02630
LS refinement shellResolution: 1.95→1.999 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.248 123 -
Rwork0.236 2340 -
obs--98.64 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more