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- PDB-1fi8: RAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD] -

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Basic information

Entry
Database: PDB / ID: 1fi8
TitleRAT GRANZYME B [N66Q] COMPLEXED TO ECOTIN [81-84 IEPD]
Components
  • (ECOTIN) x 2
  • NATURAL KILLER CELL PROTEASE 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / complex (serine protease-inhibitor) / protease substrate interactions / beta strand structure / chymotrypsin fold / granzyme B / ecotin / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Activation, myristolyation of BID and translocation to mitochondria / granzyme B / Pyroptosis / granzyme-mediated programmed cell death signaling pathway / cytolytic granule / positive regulation of necroptotic process / natural killer cell mediated cytotoxicity / pyroptotic inflammatory response / serine-type peptidase activity / protein maturation ...Activation, myristolyation of BID and translocation to mitochondria / granzyme B / Pyroptosis / granzyme-mediated programmed cell death signaling pathway / cytolytic granule / positive regulation of necroptotic process / natural killer cell mediated cytotoxicity / pyroptotic inflammatory response / serine-type peptidase activity / protein maturation / proteolysis involved in protein catabolic process / serine-type endopeptidase inhibitor activity / defense response / T cell mediated cytotoxicity / outer membrane-bounded periplasmic space / neuron apoptotic process / killing of cells of another organism / early endosome / negative regulation of translation / defense response to bacterium / serine-type endopeptidase activity / protein homodimerization activity / extracellular space / cytoplasm
Similarity search - Function
Ecotin, trypsin inhibitor / Ecotin, trypsin inhibitor / Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / Few Secondary Structures / Irregular ...Ecotin, trypsin inhibitor / Ecotin, trypsin inhibitor / Ecotin / Ecotin, C-terminal / Proteinase inhibitor I11, ecotin / Proteinase inhibitor I11, ecotin, gammaproteobacteria / Ecotin superfamily / Ecotin / Few Secondary Structures / Irregular / 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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsWaugh, S.M. / Harris, J.L. / Fletterick, R.J. / Craik, C.S.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The structure of the pro-apoptotic protease granzyme B reveals the molecular determinants of its specificity
Authors: Waugh, S.M. / Harris, J.L. / Fletterick, R. / Craik, C.S.
History
DepositionAug 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NATURAL KILLER CELL PROTEASE 1
C: ECOTIN
D: ECOTIN
B: NATURAL KILLER CELL PROTEASE 1
E: ECOTIN
F: ECOTIN


Theoretical massNumber of molelcules
Total (without water)82,8006
Polymers82,8006
Non-polymers00
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17410 Å2
ΔGint-90 kcal/mol
Surface area29350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.64, 154.6, 57.24
Angle α, β, γ (deg.)90, 119.76, 90
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly is the tetramer in the asymmetric unit.

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Components

#1: Protein NATURAL KILLER CELL PROTEASE 1 / GRANZYME B


Mass: 25225.396 Da / Num. of mol.: 2 / Mutation: N66Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Description: CYTOTOXIC LYMPHOCYTE GRANULES / Plasmid: PPICZAA / Production host: Pichia pastoris (fungus)
References: UniProt: P18291, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein ECOTIN


Mass: 9528.733 Da / Num. of mol.: 2 / Fragment: RESIDUES 28 - 111 / Mutation: V81I, S82E, T83P, M84D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTACTAC / Production host: Escherichia coli (E. coli) / References: UniProt: P23827
#3: Protein ECOTIN


Mass: 6645.746 Da / Num. of mol.: 2 / Fragment: RESIDUES 112 - 169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTACTAC / Production host: Escherichia coli (E. coli) / References: UniProt: P23827
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: sodium acetate, PEGmme 2000, ammonium acetate,, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150-1500 mM1dropNaCl
25 mg/mlprotein1drop
3100 mMsodium acetate1reservoirpH5.8
4100 mMammonium sulfate1reservoir
525 %(w/v)PEG2000MME1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1851
2851
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL9-111.08
SYNCHROTRONSSRL BL7-121.08
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEAug 3, 1999
MARRESEARCH2IMAGE PLATENov 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→35.8 Å / Num. all: 98218 / Num. obs: 98218 / % possible obs: 90.3 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 6.8
Reflection shellResolution: 2.21→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.58 / Num. unique all: 48837 / % possible all: 90.7
Reflection
*PLUS
Num. obs: 48837 / Num. measured all: 121975
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.2→35.7 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
Details: Crystal 1 data was used for initial molecular replacement and refinement. Crystal 2 data was given the same Rfree set and used for final refinement. Molecular replacement used 1AZZ and 1AUG.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1305 0.05 %5% of observed reflections
Rwork0.218 ---
obs0.222 25137 90.2 %-
all-27853 --
Displacement parametersBiso mean: 43.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.42 Å
Luzzati sigma a0.5 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.2→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5268 0 0 370 5638
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 35.7 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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