[English] 日本語
Yorodumi
- PDB-9h60: Leishmania braziliensis ISP2 in complex with bovine alpha-chymotrypsin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h60
TitleLeishmania braziliensis ISP2 in complex with bovine alpha-chymotrypsin
Components
  • Chymotrypsinogen A
  • Ecotin-like protein 2
KeywordsHYDROLASE / ecotin-like inhibitor / complex / protease / Leishmania
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Ecotin superfamily / Ecotin / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. ...Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Ecotin superfamily / Ecotin / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Ecotin-like protein 2 / Chymotrypsinogen A
Similarity search - Component
Biological speciesLeishmania braziliensis (eukaryote)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFreitag-Pohl, S. / Pohl, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MR/P027989/1 United Kingdom
CitationJournal: To Be Published
Title: Deciphering the Interactions of Leishmanial Serine Protease Inhibitors ISP2 and Proteases
Authors: Freitag-Pohl, S. / Pohl, E.
History
DepositionOct 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ecotin-like protein 2
B: Chymotrypsinogen A
C: Ecotin-like protein 2
D: Chymotrypsinogen A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,66344
Polymers86,6734
Non-polymers2,98940
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.276, 92.086, 96.519
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21C
32B
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAMETMETAA14 - 15814 - 158
211ALAALAMETMETCC14 - 15814 - 158
322CYSCYSASNASNBB1 - 2451 - 245
422CYSCYSASNASNDD1 - 2451 - 245

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Ecotin-like protein 2


Mass: 17650.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania braziliensis (eukaryote) / Strain: BA788 / Gene: LbrM15_V2.0540, LbrM_15_0540 / Production host: Escherichia coli (E. coli) / References: UniProt: A4H823
#2: Protein Chymotrypsinogen A


Mass: 25686.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00766, chymotrypsin

-
Non-polymers , 6 types, 346 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.44 % / Description: plate
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Potassium bromide 0.1 M Sodium acetate pH 5.5 25 % w/v PEG 2000 MME

-
Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979499 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 1.9→53.88 Å / Num. obs: 64941 / % possible obs: 100 % / Redundancy: 27.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.03 / Rrim(I) all: 0.154 / Χ2: 0.99 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 27 % / Rmerge(I) obs: 1.865 / Mean I/σ(I) obs: 1 / Num. unique obs: 3196 / CC1/2: 0.844 / Rpim(I) all: 0.36 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→53.873 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.521 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2175 3275 5.049 %
Rwork0.181 61586 -
all0.183 --
obs-64861 99.86 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 39.215 Å2
Baniso -1Baniso -2Baniso -3
1-0.917 Å2-0 Å2-0 Å2
2--2.168 Å2-0 Å2
3----3.085 Å2
Refinement stepCycle: LAST / Resolution: 1.9→53.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5607 0 196 306 6109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125941
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165492
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.7928059
X-RAY DIFFRACTIONr_angle_other_deg0.4891.72312699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6115761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.582520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6710868
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.34910204
X-RAY DIFFRACTIONr_chiral_restr0.0660.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021265
X-RAY DIFFRACTIONr_nbd_refined0.2020.2996
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.25012
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22885
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.23235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2305
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1240.213
X-RAY DIFFRACTIONr_nbd_other0.1980.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.29
X-RAY DIFFRACTIONr_mcbond_it3.343.7993047
X-RAY DIFFRACTIONr_mcbond_other3.233.7853032
X-RAY DIFFRACTIONr_mcangle_it4.3356.7773776
X-RAY DIFFRACTIONr_mcangle_other4.3346.7773777
X-RAY DIFFRACTIONr_scbond_it4.2184.1422894
X-RAY DIFFRACTIONr_scbond_other4.2184.1422895
X-RAY DIFFRACTIONr_scangle_it5.8797.4264276
X-RAY DIFFRACTIONr_scangle_other5.8787.4254277
X-RAY DIFFRACTIONr_lrange_it7.34738.5646326
X-RAY DIFFRACTIONr_lrange_other7.34938.5616327
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.053722
X-RAY DIFFRACTIONr_ncsr_local_group_20.0880.057203
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.091390.05008
12AX-RAY DIFFRACTIONLocal ncs0.091390.05008
23AX-RAY DIFFRACTIONLocal ncs0.088090.05009
24AX-RAY DIFFRACTIONLocal ncs0.088090.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9470.2652410.274423X-RAY DIFFRACTION98.709
1.947-20.2662100.2454412X-RAY DIFFRACTION100
2-2.0580.2732150.2244287X-RAY DIFFRACTION99.9778
2.058-2.1220.2452270.2054146X-RAY DIFFRACTION100
2.122-2.1910.232410.1883992X-RAY DIFFRACTION100
2.191-2.2680.2342040.1753887X-RAY DIFFRACTION100
2.268-2.3530.2322190.1753749X-RAY DIFFRACTION100
2.353-2.4490.2412510.1753582X-RAY DIFFRACTION99.9739
2.449-2.5580.2061760.1743504X-RAY DIFFRACTION100
2.558-2.6820.2011630.1613342X-RAY DIFFRACTION99.943
2.682-2.8270.1871570.1593181X-RAY DIFFRACTION100
2.827-2.9980.2041870.1632983X-RAY DIFFRACTION100
2.998-3.2040.181120.1562887X-RAY DIFFRACTION100
3.204-3.460.2131500.1672638X-RAY DIFFRACTION100
3.46-3.7890.1961160.1672478X-RAY DIFFRACTION100
3.789-4.2330.214780.1722273X-RAY DIFFRACTION100
4.233-4.8830.2231270.1641965X-RAY DIFFRACTION99.9522
4.883-5.9690.2061170.1891674X-RAY DIFFRACTION100
5.969-8.390.238600.2111358X-RAY DIFFRACTION100
8.39-53.8730.235230.248825X-RAY DIFFRACTION99.1813

+
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://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