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- PDB-9j91: Structures and mechanisms of serine protease inhibitors of Trichi... -

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Basic information

Entry
Database: PDB / ID: 9j91
TitleStructures and mechanisms of serine protease inhibitors of Trichinella spiralis and Trichinella pseudospiralis
ComponentsSerine protease inhibitor 1 serpin
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 protease inhibitor 1 serpin
Similarity search - Component
Biological speciesTrichinella pseudospiralis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease inhibitor 1 serpin


Theoretical massNumber of molelcules
Total (without water)42,7331
Polymers42,7331
Non-polymers00
Water48627
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)175.498, 175.498, 63.425
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

21A-420-

HOH

31A-425-

HOH

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Components

#1: Protein Serine protease inhibitor 1 serpin


Mass: 42732.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichinella pseudospiralis (invertebrata)
Production host: Escherichia coli (E. coli) / References: UniProt: G3FZ83
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 289.1 K / Method: vapor diffusion, hanging drop
Details: 22% polyethylene glycol 8K, 0.2 M sodium chloride, 0.1 M sodium acetate trihydrate, pH 4.0, 30% w/v D-(+)-Glucose monohydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97913 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: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.6→29.27 Å / Num. obs: 18284 / % possible obs: 99.8 % / Redundancy: 19.8 % / Biso Wilson estimate: 58.87 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Net I/σ(I): 20
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 1.64 / Num. unique obs: 1772 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.27 Å / SU ML: 0.418 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.5463
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2925 883 4.83 %
Rwork0.2606 17400 -
obs0.2623 18283 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.82 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 0 27 2586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912609
X-RAY DIFFRACTIONf_angle_d1.22773515
X-RAY DIFFRACTIONf_chiral_restr0.0653398
X-RAY DIFFRACTIONf_plane_restr0.0059446
X-RAY DIFFRACTIONf_dihedral_angle_d12.9418333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.4271310.30982847X-RAY DIFFRACTION99.77
2.76-2.970.30951380.29232848X-RAY DIFFRACTION100
2.97-3.270.34741510.29552848X-RAY DIFFRACTION100
3.27-3.740.30911500.28252884X-RAY DIFFRACTION100
3.74-4.710.25361520.23442902X-RAY DIFFRACTION99.97
4.71-100.27881610.24523071X-RAY DIFFRACTION99.88

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