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- PDB-9j88: Structures and mechanisms of serine protease inhibitors of Trichi... -

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Basic information

Entry
Database: PDB / ID: 9j88
TitleStructures and mechanisms of serine protease inhibitors of Trichinella spiralis and Trichinella pseudospiralis
ComponentsSerine proteinase inhibitor
KeywordsSTRUCTURAL PROTEIN / Trichinella spiralis / serine protease inhibitor / crystal structure / vaccines
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
Serine proteinase inhibitor
Similarity search - Component
Biological speciesTrichinella spiralis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsChen, C. / Xue, L.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structures and mechanisms of serine protease inhibitors of Trichinella spiralis and Trichinella pseudospiralis
Authors: Chen, C. / Xue, L.R.
History
DepositionAug 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Serine proteinase inhibitor
A: Serine proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)84,9232
Polymers84,9232
Non-polymers00
Water63135
1
B: Serine proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)42,4621
Polymers42,4621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Serine proteinase inhibitor


Theoretical massNumber of molelcules
Total (without water)42,4621
Polymers42,4621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.547, 71.626, 143.699
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Serine proteinase inhibitor / Serpin B9


Mass: 42461.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichinella spiralis (invertebrata) / Gene: SERPINB9, T01_4475 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NH65
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.83 Å3/Da / Density % sol: 32.95 %
Crystal growTemperature: 289.1 K / Method: vapor diffusion, hanging drop
Details: 32% polyethylene glycol 8K, 0.15 M ammonium sulfate, 0.2 M sodium cacodylate trihydrate, pH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.34→30.27 Å / Num. obs: 26731 / % possible obs: 99.05 % / Redundancy: 9.5 % / Biso Wilson estimate: 54.3 Å2 / CC1/2: 0.99 / Net I/σ(I): 18.3
Reflection shellResolution: 2.34→2.43 Å / Num. unique obs: 2449 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→29.62 Å / SU ML: 0.3778 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 34.4226 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.287 1344 5.03 %
Rwork0.2227 25365 -
obs0.2261 26709 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.59 Å2
Refinement stepCycle: LAST / Resolution: 2.34→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5311 0 0 35 5346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00985429
X-RAY DIFFRACTIONf_angle_d1.12757325
X-RAY DIFFRACTIONf_chiral_restr0.0571815
X-RAY DIFFRACTIONf_plane_restr0.0068919
X-RAY DIFFRACTIONf_dihedral_angle_d4.05533231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.430.33791140.26542303X-RAY DIFFRACTION91.31
2.43-2.520.42621260.27222523X-RAY DIFFRACTION99.62
2.52-2.640.34511410.26912513X-RAY DIFFRACTION99.89
2.64-2.780.39511300.25982526X-RAY DIFFRACTION99.96
2.78-2.950.31431190.24942536X-RAY DIFFRACTION99.96
2.95-3.180.3361220.24542563X-RAY DIFFRACTION100
3.18-3.50.29171340.24662555X-RAY DIFFRACTION100
3.5-40.31291590.21172569X-RAY DIFFRACTION100
4-5.040.23591440.18782596X-RAY DIFFRACTION100
5.04-6.150.25391550.21352681X-RAY DIFFRACTION98.95

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