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- PDB-8pi2: Native alpha-1-antitrypsin at 1.5 Angstrom (Cys232Ser) -

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Basic information

Entry
Database: PDB / ID: 8pi2
TitleNative alpha-1-antitrypsin at 1.5 Angstrom (Cys232Ser)
ComponentsAlpha-1-antitrypsin
KeywordsPROTEIN BINDING / Antitrypsin / protease inhibitor / serpin / native
Function / homology
Function and homology information


Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / 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-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / 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
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
Similarity search - Domain/homology
GLYCINE / Alpha-1-antitrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsWang, M. / Irving, J.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V034243/1 United Kingdom
Other privateAlpha-1 Foundation to JI
CitationJournal: To Be Published
Title: Structural determinants of instability in alpha-1-antitrypsin
Authors: Aldobiyan, I. / Wang, M. / Irving, J.A. / Lomas, D.A.
History
DepositionJun 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)45,8114
Polymers45,5961
Non-polymers2153
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.566, 38.994, 89.247
Angle α, β, γ (deg.)90.000, 103.880, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 45595.680 Da / Num. of mol.: 1 / Mutation: C232S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Organ: Liver / Plasmid: pQE-31 / Details (production host): T5 / Production host: Escherichia coli K-12 (bacteria) / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42.8 % / Description: Plate
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.75 / Details: 0.1M malonate-imidazole-borate pH5.75, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2020
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.48→86.64 Å / Num. obs: 63873 / % possible obs: 99.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 21.37 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.06 / Rrim(I) all: 0.109 / Χ2: 0.43 / Net I/σ(I): 5.4
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.414 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3170 / CC1/2: 0.297 / Rpim(I) all: 0.923 / Rrim(I) all: 1.695 / Χ2: 0.42 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.4data scaling
autoPROC1.0.5data processing
XDS20200417data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→55.61 Å / SU ML: 0.2376 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1117
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 1996 3.13 %
Rwork0.1685 61718 -
obs0.1693 63714 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.98 Å2
Refinement stepCycle: LAST / Resolution: 1.48→55.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 13 325 3166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00393000
X-RAY DIFFRACTIONf_angle_d0.73174092
X-RAY DIFFRACTIONf_chiral_restr0.0642485
X-RAY DIFFRACTIONf_plane_restr0.0064524
X-RAY DIFFRACTIONf_dihedral_angle_d16.81861094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.41261400.36494334X-RAY DIFFRACTION98.35
1.52-1.560.36331420.31124392X-RAY DIFFRACTION99.21
1.56-1.60.28661420.25534365X-RAY DIFFRACTION99.01
1.6-1.660.28891410.22544368X-RAY DIFFRACTION99.6
1.66-1.710.25071440.2044426X-RAY DIFFRACTION99.43
1.71-1.780.25441410.19874412X-RAY DIFFRACTION99.76
1.78-1.860.26991430.19734400X-RAY DIFFRACTION99.56
1.86-1.960.21541430.18184397X-RAY DIFFRACTION99.63
1.96-2.090.20861430.14664450X-RAY DIFFRACTION99.83
2.09-2.250.18821430.14084411X-RAY DIFFRACTION99.67
2.25-2.470.18961430.1474436X-RAY DIFFRACTION99.52
2.47-2.830.17921430.15534440X-RAY DIFFRACTION98.94
2.83-3.570.18781430.16034427X-RAY DIFFRACTION98.2
3.57-55.610.14811450.1574460X-RAY DIFFRACTION96.68

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