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- PDB-6iay: Alpha-1-antitrypsin Queen's (Lys154Asn) variant -

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Basic information

Entry
Database: PDB / ID: 6iay
TitleAlpha-1-antitrypsin Queen's (Lys154Asn) variant
ComponentsAlpha-1-antitrypsin
KeywordsPROTEIN BINDING / Antitrypsin / protease inhibitor / serpin / mutant / deficiency
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / 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 ...Cargo concentration in the ER / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / platelet alpha granule lumen / acute-phase response / Post-translational protein phosphorylation / 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 / protease binding / : / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / Golgi apparatus / extracellular space / extracellular exosome / extracellular region / identical protein 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 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GLYCINE / Alpha-1-antitrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsAldobiyan, I. / Lomas, D.A. / Irving, J.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N024842/1 United Kingdom
Other governmentUCLH/NIHR Biomedical Research Centre United Kingdom
CitationJournal: To Be Published
Title: Structural determinants of instability in alpha-1-antitrypsin
Authors: Aldobiyan, I. / Irving, J.A. / Lomas, D.A.
History
DepositionNov 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-1-antitrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6562
Polymers45,5811
Non-polymers751
Water3,783210
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.265, 38.763, 89.712
Angle α, β, γ (deg.)90.000, 104.130, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-1-antitrypsin / Alpha-1 protease inhibitor / Alpha-1-antiproteinase / Serpin A1


Mass: 45580.602 Da / Num. of mol.: 1 / Mutation: K154N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Plasmid: pQE30 / Details (production host): T5 promoter / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): XL-1 Blue / References: UniProt: P01009
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.33 Å3/Da / Density % sol: 47.11 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 22.5% PEG 1500, 0.1M SPG (succinate-phosphate-glycine) pH 5.75

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 21, 2018 / Details: Compound refractive lenses
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→43.51 Å / Num. obs: 29809 / % possible obs: 98.1 % / Redundancy: 3.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.035 / Rrim(I) all: 0.063 / Χ2: 0.94 / Net I/av σ(I): 9.6 / Net I/σ(I): 9.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.953.30.5141.921890.5260.3310.6140.7497.1
8.5-43.5130.02631.13740.9990.0170.031198.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.73 Å43.5 Å

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHASER2.8.2phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.24data extraction
DIALS1.9.3-gb491019a-releasedata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I4V

6i4v


Resolution: 1.9→43.499 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 29.73
RfactorNum. reflection% reflection
Rfree0.2415 1536 5.16 %
Rwork0.212 --
obs0.2136 29795 97.58 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 93.59 Å2 / Biso mean: 42.4872 Å2 / Biso min: 20.03 Å2
Refinement stepCycle: final / Resolution: 1.9→43.499 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 5 212 3009
Biso mean--53.53 46.48 -
Num. residues----368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8995-1.96080.36931710.36092476264796
1.9608-2.03090.3251210.31022535265697
2.0309-2.11220.30631310.2762527265897
2.1122-2.20840.32591450.26462533267897
2.2084-2.32480.30721500.25342553270397
2.3248-2.47040.33411450.23722510265597
2.4704-2.66120.24321150.2262588270398
2.6612-2.92890.29511300.21762598272898
2.9289-3.35260.25171420.21862596273898
3.3526-4.22340.19881490.18732624277399
4.2234-43.51080.19051370.17642719285699

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