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- PDB-9h6o: Leishmania major ISP2 in complex with bovine alpha-chymotrypsin -

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Basic information

Entry
Database: PDB / ID: 9h6o
TitleLeishmania major 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


symbiont-mediated suppression of host complement activation / 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
Proteinase inhibitor I11, ecotin, gammaproteobacteria / 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. ...Proteinase inhibitor I11, ecotin, gammaproteobacteria / 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 / Chymotrypsinogen A / Ecotin-like protein 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Leishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,7129
Polymers87,1134
Non-polymers5995
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-28 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.828, 86.776, 96.69
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11D
21D
32D
42D

NCS domain segments:

Auth asym-ID: D / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth seq-IDLabel seq-ID
111CYSCYSASNASN1 - 2451 - 245
211CYSCYSASNASN1 - 2451 - 245
322VALVALALAALA17 - 15817 - 158
422VALVALALAALA17 - 15817 - 158

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

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Components

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Protein , 2 types, 4 molecules DBCA

#1: 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
#2: Protein Ecotin-like protein 2


Mass: 17870.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF15.0510, LmjF_15_0510 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QFD4

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Non-polymers , 4 types, 221 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 40.48 % / Description: block
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Sodium citrate tribasic dehydrate 0.1MBis-Tris propane 6.5 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.969384 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969384 Å / Relative weight: 1
ReflectionResolution: 1.8→86.99 Å / Num. obs: 67615 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.029 / Rrim(I) all: 0.106 / Χ2: 0.94 / Net I/σ(I): 12.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 13.3 % / Rmerge(I) obs: 2.384 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3952 / CC1/2: 0.778 / Rpim(I) all: 0.679 / Rrim(I) all: 2.482 / Χ2: 0.78 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→64.27 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.999 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.147
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.268 3468 5.136 %
Rwork0.2193 64060 -
all0.222 --
obs-67528 99.935 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.115 Å2
Baniso -1Baniso -2Baniso -3
1-2.015 Å20 Å20 Å2
2--2.22 Å2-0 Å2
3----4.235 Å2
Refinement stepCycle: LAST / Resolution: 1.8→64.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5423 0 40 216 5679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125635
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165096
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.7877717
X-RAY DIFFRACTIONr_angle_other_deg0.5841.7211759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9595749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.703523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38110806
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.13710195
X-RAY DIFFRACTIONr_chiral_restr0.0810.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026691
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021249
X-RAY DIFFRACTIONr_nbd_refined0.2050.2951
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.24814
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22788
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0910.23067
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1710.210
X-RAY DIFFRACTIONr_nbd_other0.2170.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.210
X-RAY DIFFRACTIONr_mcbond_it3.6973.8752974
X-RAY DIFFRACTIONr_mcbond_other3.6853.8732972
X-RAY DIFFRACTIONr_mcangle_it4.7716.9323699
X-RAY DIFFRACTIONr_mcangle_other4.7716.9323700
X-RAY DIFFRACTIONr_scbond_it4.3274.1052661
X-RAY DIFFRACTIONr_scbond_other4.3144.1042660
X-RAY DIFFRACTIONr_scangle_it5.8737.4334008
X-RAY DIFFRACTIONr_scangle_other5.8587.4314006
X-RAY DIFFRACTIONr_lrange_it7.17638.9446040
X-RAY DIFFRACTIONr_lrange_other7.17538.9456041
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.057009
X-RAY DIFFRACTIONr_ncsr_local_group_20.110.053542
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11DX-RAY DIFFRACTIONLocal ncs0.086980.05009
12DX-RAY DIFFRACTIONLocal ncs0.086980.05009
23DX-RAY DIFFRACTIONLocal ncs0.110020.05009
24DX-RAY DIFFRACTIONLocal ncs0.110020.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.4252350.38246880.38449340.8680.86799.77710.378
1.847-1.8970.3492640.34945330.34947980.8830.89699.97920.34
1.897-1.9520.3312460.31244320.31346790.8980.91599.97860.296
1.952-2.0120.3362460.27842980.28145460.9230.94299.9560.26
2.012-2.0780.2822760.25541360.25744120.9350.9521000.235
2.078-2.1510.2812500.23140200.23442730.9420.96299.92980.208
2.151-2.2320.2951940.21739340.22141280.9380.9681000.196
2.232-2.3230.2971980.21737900.22139880.9420.9681000.193
2.323-2.4260.2911740.21336280.21738020.9450.9711000.189
2.426-2.5440.2882000.21434900.21836900.9480.9731000.189
2.544-2.6820.2721760.21932910.22134670.9510.971000.195
2.682-2.8440.3121610.21631280.2232900.9410.97199.96960.198
2.844-3.040.2641430.21229680.21431110.950.971000.2
3.04-3.2830.2571450.21927650.22129100.9610.9671000.214
3.283-3.5960.2451420.20425710.20627130.9650.9741000.207
3.596-4.0180.2281190.20123060.20224250.9630.9741000.211
4.018-4.6370.228830.17320980.17621810.9650.9811000.192
4.637-5.6720.225940.18817660.1918600.970.9781000.21
5.672-7.990.248950.21613710.21814660.9550.9691000.243
7.99-64.270.289270.2488470.258780.9490.9699.54440.295

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