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- PDB-7vlj: Crystal structure of Entamoeba histolytica serine protease inhibi... -

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Basic information

Entry
Database: PDB / ID: 7vlj
TitleCrystal structure of Entamoeba histolytica serine protease inhibitor, Histopin, in the cleaved conformation
Components(Serine protease inhibitor, ...) x 2
KeywordsHYDROLASE / Serine protease inhibitor / Serine endopeptidases / Peptidase inhibitors / Serpin family I4
Function / homology
Function and homology information


negative regulation of endopeptidase activity / serine-type endopeptidase inhibitor activity / peptidase activity / extracellular space
Similarity search - Function
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
: / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Serine protease inhibitor, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsAli, M.F. / Devi, S. / Gourinath, S.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)PDF/2017/002157 India
CitationJournal: To Be Published
Title: Crystal structure of Entamoeba histolytica serine protease inhibitor, Histopin, in the cleaved conformation
Authors: Ali, M.F. / Devi, S. / Gourinath, S.
History
DepositionOct 3, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 17, 2021ID: 6LY2
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease inhibitor, putative
B: Serine protease inhibitor, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,93417
Polymers43,7332
Non-polymers1,20015
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-39 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.130, 61.010, 137.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Serine protease inhibitor, ... , 2 types, 2 molecules AB

#1: Protein Serine protease inhibitor, putative


Mass: 37760.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_119330 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus / References: UniProt: C4M4Y1
#2: Protein/peptide Serine protease inhibitor, putative


Mass: 5972.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_119330 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus / References: UniProt: C4M4Y1

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Non-polymers , 5 types, 233 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.96 Å3/Da / Density % sol: 37.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 25% Polyethylene glycol monomethyl ether 2000, 0.2M Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 7, 2018
RadiationMonochromator: single Silicon (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.83→45.64 Å / Num. obs: 29415 / % possible obs: 98.5 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.2
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 7.1 % / Num. unique obs: 1673 / CC1/2: 0.977 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NDA

3nda


Resolution: 1.83→45.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.411 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1508 5.1 %RANDOM
Rwork0.1568 ---
obs0.1591 27803 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.13 Å2 / Biso mean: 18.274 Å2 / Biso min: 7.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0 Å2
2---0.64 Å20 Å2
3---0.88 Å2
Refinement stepCycle: final / Resolution: 1.83→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 73 218 3217
Biso mean--35.86 26.16 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133044
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172936
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.6424074
X-RAY DIFFRACTIONr_angle_other_deg1.4561.5776780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15124.295149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19415555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.3751510
X-RAY DIFFRACTIONr_chiral_restr0.0880.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023335
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02677
LS refinement shellResolution: 1.83→1.878 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 114 -
Rwork0.166 1926 -
all-2040 -
obs--93.88 %

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