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- PDB-6i7u: Alpha-1-antitrypsin (Ala250Met) in the native conformation -

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Basic information

Entry
Database: PDB / ID: 6i7u
TitleAlpha-1-antitrypsin (Ala250Met) in the native conformation
ComponentsAlpha-1-antitrypsinAlpha-1 antitrypsin
KeywordsPROTEIN BINDING / Antitrypsin / protease inhibitor / serpin / mutant / deficiency / breach region
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 / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)45,6721
Polymers45,6721
Non-polymers00
Water7,044391
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 area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.710, 38.821, 89.322
Angle α, β, γ (deg.)90.000, 103.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-713-

HOH

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Components

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


Mass: 45671.859 Da / Num. of mol.: 1 / Mutation: A250M
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 47.21 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 22.5% PEG 1500, 0.1M SPG (succinate-phosphate-glycine) pH 5.5

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Data collection

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-IDSerial crystal experiment
1100Cryostream1N
2100Cryostream1N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I2410.9686
SYNCHROTRONDiamond I0420.9795
Detector
TypeIDDetectorDateDetails
DECTRIS PILATUS 6M1PIXELMay 5, 2018Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors
DECTRIS PILATUS 6M-F2PIXELMay 22, 2018Compound refractive lenses
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double crystal Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97951
ReflectionResolution: 1.55→86.73 Å / Num. obs: 55773 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 21.29 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.047 / Rrim(I) all: 0.117 / Χ2: 0.93 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.584.90.9241.826930.7440.4711.0431.199.9
8.49-86.735.30.09115.73850.9920.0420.11.2799.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.48 Å53.11 Å
Translation5.48 Å53.11 Å

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Processing

Software
NameVersionClassification
XDSNovember 11, 2017data reduction
Aimless0.6.2data scaling
PHASER2.8.1phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.24data extraction
autoPROC1.0.5data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I4V

6i4v


Resolution: 1.55→36.658 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.35
RfactorNum. reflection% reflection
Rfree0.2109 2841 5.1 %
Rwork0.1862 --
obs0.1875 55693 99.64 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 107.07 Å2 / Biso mean: 33.2257 Å2 / Biso min: 13.18 Å2
Refinement stepCycle: final / Resolution: 1.55→36.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 0 391 3230
Biso mean---39.86 -
Num. residues----372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.57680.32081360.297425762712100
1.5768-1.60540.33471540.279626332787100
1.6054-1.63630.26881390.256826412780100
1.6363-1.66970.26431340.242426132747100
1.6697-1.7060.26821300.232726462776100
1.706-1.74570.24281340.238226452779100
1.7457-1.78940.28371590.231426092768100
1.7894-1.83780.22391290.22426642793100
1.8378-1.89180.25961480.2226122760100
1.8918-1.95290.26671780.23672603278199
1.9529-2.02270.241390.202225982737100
2.0227-2.10370.22761230.194926472770100
2.1037-2.19940.22041530.189426332786100
2.1994-2.31530.251460.2012585273197
2.3153-2.46040.20491460.186526552801100
2.4604-2.65030.19751260.18726822808100
2.6503-2.91690.22171330.181326712804100
2.9169-3.33870.21791440.178426712815100
3.3387-4.20550.16611500.1552667281799
4.2055-36.66780.16741400.156328012941100

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