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- PDB-8r13: Alpha-1-antitrypsin (Met374Phe) in the native conformation -

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Basic information

Entry
Database: PDB / ID: 8r13
TitleAlpha-1-antitrypsin (Met374Phe) in the native conformation
ComponentsAlpha-1-antitrypsin
KeywordsPROTEIN BINDING / Antitrypsin / protease inhibitor / serpin / mutant / deficiency / small molecule
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAldobiyan, I. / Lomas, D.A. / Irving, J.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V034243/1 United Kingdom
Other governmentNIHR investigator award to DAL
Other privateAlpha-1 Foundation to JAI 1036784
CitationJournal: To Be Published
Title: Structural determinants of instability in alpha-1-antitrypsin
Authors: Aldobiyan, I. / Irving, J.A. / Lomas, D.A.
History
DepositionNov 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)45,6281
Polymers45,6281
Non-polymers00
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, also native gel
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.982, 38.657, 89.244
Angle α, β, γ (deg.)90.000, 104.179, 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


Mass: 45627.719 Da / Num. of mol.: 1 / Mutation: M374F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1 / Plasmid: pQE30 / Details (production host): T5 promoter / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue / References: UniProt: P01009
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.11 Å3/Da / Density % sol: 41.63 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 22.5% PEG 1500, 0.1M MIB (malonate-imidazole-borate) pH 5.25

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2018 / Details: Vertical CRL / Horizontal Eliptical mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.95→86.53 Å / Num. obs: 27080 / % possible obs: 96.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 30.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.031 / Rrim(I) all: 0.055 / Χ2: 0.88 / Net I/σ(I): 13.7 / Num. measured all: 84082
Reflection shellResolution: 1.95→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.326 / Num. unique obs: 1855 / CC1/2: 0.971 / Rpim(I) all: 0.223 / Rrim(I) all: 0.396 / Χ2: 0.91

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.6.2data scaling
XDS20180126data reduction
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→55.74 Å / SU ML: 0.1975 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.206
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 1349 5.03 %
Rwork0.2091 25455 -
obs0.2105 26804 95.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.95 Å2
Refinement stepCycle: LAST / Resolution: 1.95→55.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 0 231 2993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022907
X-RAY DIFFRACTIONf_angle_d0.48413972
X-RAY DIFFRACTIONf_chiral_restr0.0397476
X-RAY DIFFRACTIONf_plane_restr0.0032510
X-RAY DIFFRACTIONf_dihedral_angle_d14.85231031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.31471400.30042533X-RAY DIFFRACTION96.74
2.02-2.10.25891210.23782609X-RAY DIFFRACTION98.56
2.1-2.20.32311520.26852481X-RAY DIFFRACTION94.75
2.2-2.310.55811140.44952133X-RAY DIFFRACTION80.05
2.31-2.460.29631510.2352609X-RAY DIFFRACTION98.29
2.46-2.650.21531230.22162653X-RAY DIFFRACTION99.11
2.65-2.910.25221310.20932629X-RAY DIFFRACTION98.29
2.91-3.330.22181430.20272631X-RAY DIFFRACTION98.13
3.33-4.20.1651380.17172429X-RAY DIFFRACTION90.39
4.2-55.740.19851360.16552748X-RAY DIFFRACTION97.83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.32185028732-0.7952837309260.01125330826551.91546889831-0.6496805437492.1611182617-0.0797248113680.09740680923130.2347073196340.1145546188750.0908054416075-0.122522801349-0.08821570221130.190628365348-0.02908934330350.2509633274330.02724737579520.02780780795230.222028096611-0.05752925288370.17941590943724.31948881390.15795810810716.845229373
23.76702085992-0.586684793417-1.967678394881.161222984930.8411468204922.528535246220.0447605530290.1217182038540.01710945719440.0328791491799-0.0008858235472050.1063105022560.01513188781790.000177505853928-0.04647962338710.2049748575530.011583099473-0.009579984424490.1197385044170.03416735349510.1562608593847.52013504238-0.4758992947227.2612923421
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 24 through 174 )24 - 1741 - 149
22chain 'A' and (resid 175 through 393 )175 - 393150 - 363

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