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- PDB-1k9o: CRYSTAL STRUCTURE OF MICHAELIS SERPIN-TRYPSIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1k9o
TitleCRYSTAL STRUCTURE OF MICHAELIS SERPIN-TRYPSIN COMPLEX
Components
  • ALASERPIN
  • TRYPSIN II ANIONIC
KeywordsHydrolase/Hydrolase Inhibitor / Michaelis serpin-protease complex inhibitory triad / Hydrolase-Hydrolase Inhibitor COMPLEX
Function / homology
Function and homology information


Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / response to bacterium / serine-type endopeptidase inhibitor activity ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / Neutrophil degranulation / collagen catabolic process / trypsin / digestion / response to nutrient / response to bacterium / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / 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 / : / 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 / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Anionic trypsin-2 / Alaserpin
Similarity search - Component
Biological speciesManduca sexta (tobacco hornworm)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYe, S. / Cech, A.L. / Belmares, R. / Bergstrom, R.C. / Tong, Y. / Corey, D.R. / Kanost, M.R. / Goldsmith, E.J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: The structure of a Michaelis serpin-protease complex.
Authors: Ye, S. / Cech, A.L. / Belmares, R. / Bergstrom, R.C. / Tong, Y. / Corey, D.R. / Kanost, M.R. / Goldsmith, E.J.
History
DepositionOct 29, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionNov 21, 2001ID: 1I99
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: 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
I: ALASERPIN
E: TRYPSIN II ANIONIC


Theoretical massNumber of molelcules
Total (without water)65,8162
Polymers65,8162
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-11 kcal/mol
Surface area24560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.572, 112.572, 95.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11I-388-

HOH

21I-390-

HOH

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Components

#1: Protein ALASERPIN / SERPIN 1


Mass: 42016.988 Da / Num. of mol.: 1 / Mutation: A353K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Plasmid: H6PQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P14754
#2: Protein TRYPSIN II ANIONIC / PRETRYPSINOGEN II


Mass: 23798.838 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PYT / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00763, trypsin
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3350, DTT, POTASSIUM PHOSPHATE, SODIUM PHOSPHATE, 2-PROPANOL, AMMONIUM CHLORIDE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 6.5 / PH range high: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMMES1drop
3100 mM1dropNaCl
41 mMdithiothreitol1drop
51 mMEDTA1drop
61.0 M1reservoirNH4Cl
74 %(v/v)isopropanol1reservoir
80.2 Msodium potassium phosphate1reservoir
920 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorDetector: CCD / Date: Dec 10, 1999 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 30999 / % possible obs: 98.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.76 / Num. unique all: 30999 / % possible all: 95.6
Reflection
*PLUS
Num. measured all: 186342
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1SEK AND 1DPO

1sek

1dpo


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2566 -RANDOM
Rwork0.158 ---
obs-26545 84 %-
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 0 182 4786
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.61
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.61

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