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- PDB-1oph: NON-COVALENT COMPLEX BETWEEN ALPHA-1-PI-PITTSBURGH AND S195A TRYPSIN -

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Basic information

Entry
Database: PDB / ID: 1oph
TitleNON-COVALENT COMPLEX BETWEEN ALPHA-1-PI-PITTSBURGH AND S195A TRYPSIN
Components
  • Alpha-1-antitrypsin precursor
  • Trypsinogen, cationic precursor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE INHIBITOR / MICHAELIS-LIKE COMPLEX / SERPIN / ALPHA-1 ANTITRYPSIN / TRYPSIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / Post-translational protein phosphorylation / acute-phase response / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / collagen-containing extracellular matrix / endopeptidase activity / protease binding / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding
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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
Serine protease 1 / Alpha-1-antitrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDementiev, A. / Simonovic, M. / Volz, K. / Gettins, P.G.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Canonical inhibitor-like interactions explain reactivity of alpha1-proteinase inhibitor Pittsburgh and antithrombin with proteinases
Authors: Dementiev, A. / Simonovic, M. / Volz, K. / Gettins, P.G.
History
DepositionMar 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-1-antitrypsin precursor
B: Trypsinogen, cationic precursor


Theoretical massNumber of molelcules
Total (without water)69,7052
Polymers69,7052
Non-polymers00
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area24120 Å2
MethodPISA
2
A: Alpha-1-antitrypsin precursor
B: Trypsinogen, cationic precursor

A: Alpha-1-antitrypsin precursor
B: Trypsinogen, cationic precursor


Theoretical massNumber of molelcules
Total (without water)139,4104
Polymers139,4104
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5820 Å2
ΔGint-17 kcal/mol
Surface area45130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.230, 62.320, 98.880
Angle α, β, γ (deg.)90.00, 110.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-1-antitrypsin precursor / Alpha-1 protease inhibitor / Alpha-1- antiproteinase / PRO0684/PRO2209


Mass: 44276.258 Da / Num. of mol.: 1 / Fragment: alpha-1-antitrypsin (RESIDUES 26-418)
Mutation: F51L, T59A, T68A, A70G, C232S, M358R, M274I, S381A, K387R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Gene: SERPINA1 OR PI OR AAT / Plasmid: pQE30 / Cell line (production host): SG13009 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P01009
#2: Protein Trypsinogen, cationic precursor / / Beta-trypsin / Fragment


Mass: 25428.717 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pQE60 / Cell line (production host): SG13009 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P00760, trypsin
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2 M tri-K-citrate, 17.5% PEG 3350, 2% GLYCEROL, pH 8.30, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / PH range low: 8.5 / PH range high: 8.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mprotein1droppH8.3-8.5
217.5 %(w/v)PEG33501reservoir
32 %glycerol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 22-ID21
Detector
TypeIDDetectorDate
MARRESEARCH1CCDAug 27, 2002
MARRESEARCH2CCDAug 27, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 220SINGLE WAVELENGTHMx-ray1
2Si 220SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 32771 / Num. obs: 32771 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.2 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 20.6
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.75 / Num. unique all: 3330 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 100 Å / Num. obs: 33539 / % possible obs: 99.5 % / Num. measured all: 628540 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLP AND 1EJM

1qlp

1ejm


Resolution: 2.3→22.51 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3277 10 %RANDOM
Rwork0.19 ---
all-32771 --
obs-32771 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.0933 Å2 / ksol: 0.356808 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1--8.51 Å20 Å22.08 Å2
2--19.34 Å20 Å2
3----10.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.3→22.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 0 377 4919
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.3→2.41 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 362 9.9 %
Rwork0.254 4567 -
obs-3853 92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.PARAM
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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