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- PDB-8qz5: Alpha-1-antitrypsin (Tyr244Phe) in the native conformation -

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Basic information

Entry
Database: PDB / ID: 8qz5
TitleAlpha-1-antitrypsin (Tyr244Phe) 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-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
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
PHOSPHATE ION / Alpha-1-antitrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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
DepositionOct 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7392
Polymers45,6441
Non-polymers951
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-4 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.098, 38.628, 90.039
Angle α, β, γ (deg.)90.000, 104.520, 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: 45643.742 Da / Num. of mol.: 1 / Mutation: Y244F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1 / Plasmid: pQE30 / Details (production host): Lac5 / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): XL1-Blue / References: UniProt: P01009
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 41.6 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 25% 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976249 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2019 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976249 Å / Relative weight: 1
ReflectionResolution: 1.69→43.58 Å / Num. obs: 42043 / % possible obs: 98 % / Redundancy: 6.3 % / Biso Wilson estimate: 33.02 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Net I/σ(I): 9.2 / Num. measured all: 264538
Reflection shellResolution: 1.69→1.75 Å / % possible obs: 80.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 1.707 / Num. measured all: 15030 / Num. unique obs: 3378 / CC1/2: 0.599 / Rpim(I) all: 0.843 / Rrim(I) all: 1.916 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.5.27data scaling
XDS20190315data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.69→42.12 Å / SU ML: 0.2801 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.6677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2126 1876 4.53 %
Rwork0.1995 39540 -
obs0.2001 41416 96.7 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.9 Å2
Refinement stepCycle: LAST / Resolution: 1.69→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 5 193 2956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692908
X-RAY DIFFRACTIONf_angle_d0.66283971
X-RAY DIFFRACTIONf_chiral_restr0.0489473
X-RAY DIFFRACTIONf_plane_restr0.0049508
X-RAY DIFFRACTIONf_dihedral_angle_d13.35821038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.740.4586900.47251975X-RAY DIFFRACTION63.17
1.74-1.790.42471430.42253028X-RAY DIFFRACTION97.57
1.79-1.850.42381560.36393117X-RAY DIFFRACTION99.63
1.85-1.910.3471460.28563101X-RAY DIFFRACTION99.57
1.91-1.990.25641450.23973092X-RAY DIFFRACTION99.63
1.99-2.080.27741490.23363143X-RAY DIFFRACTION99.52
2.08-2.190.25391460.24213111X-RAY DIFFRACTION99.82
2.19-2.330.2131480.20353125X-RAY DIFFRACTION99.85
2.33-2.510.24731640.20323120X-RAY DIFFRACTION99.85
2.51-2.760.19211250.20543181X-RAY DIFFRACTION99.94
2.76-3.160.21791530.19653131X-RAY DIFFRACTION99.58
3.16-3.980.1841610.17783167X-RAY DIFFRACTION99.67
3.98-42.120.17021500.16343249X-RAY DIFFRACTION99.04
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)
12.02332966872-0.585098644222-0.2260114935520.784494467762-0.2744790090820.803348056808-0.05063669545140.09637550257670.1155323979860.06330075201260.115218298783-0.0135666916125-0.06585263077370.1797426576980.0005229369167710.2573969712690.022459356171-0.01689045880740.298703309054-0.02715202358050.25464902548424.25537384860.52745286985816.7273421038
22.1875604716-0.713660632514-1.193105220770.807267416070.7431036478281.52704527896-0.153576481729-0.0684316997404-0.07307405150910.1591076071290.1012060879280.09424061118550.1612337275580.11457031957-0.006122358269740.2679286756080.0607604106137-0.01493360607280.1761526833170.02166185799070.2241846575029.02117894392-1.2990971514726.2748786614
30.2678890401120.09213676864760.03659541270030.547816581160.7085339557351.363094908880.0279818620355-0.06889115891430.1413196065030.199030821572-0.05065096890210.1081996581180.2118318741190.10246266854-0.02109565677590.33268672890.02091476172870.08487209577510.1574461507440.03821778120980.3123978324082.773823438751.134800016129.3932964206
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 - 151
22chain 'A' and (resid 175 through 355 )175 - 355152 - 324
33chain 'A' and (resid 356 through 393 )356 - 393325 - 362

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