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- PDB-6i4v: Alpha-1-antitrypsin Queen's (K154N) variant -

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Basic information

Entry
Database: PDB / ID: 6i4v
TitleAlpha-1-antitrypsin Queen's (K154N) variant
ComponentsAlpha-1-antitrypsin
KeywordsPROTEIN BINDING / Antitrypsin / protease inhibitor / serpin / mutant / deficiency
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) ...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
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 / 3-trimethylsilylpropane-1-sulfonic acid / Alpha-1-antitrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 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 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-1-antitrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9274
Polymers45,5811
Non-polymers3463
Water3,513195
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 area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.460, 38.950, 89.850
Angle α, β, γ (deg.)90.000, 103.950, 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.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-H3B / 3-trimethylsilylpropane-1-sulfonic acid


Mass: 196.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16O3SSi
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 47.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 20% PEG 1500, 0.1M SPG (succinate-phosphate-glycine), 0.5mM DSS (4,4-dimethyl-4-silapentane-1-sulfonic acid)

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2018 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 1.78→52.99 Å / Num. obs: 37234 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 34.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Χ2: 1.04 / Net I/av σ(I): 13.5 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.826.71.3321.520670.6020.5541.4450.9499.8
9.08-52.995.50.03930.43150.9980.0180.0430.9698.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.44 Å52.99 Å
Translation5.44 Å52.99 Å

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Processing

Software
NameVersionClassification
XDSJan 26, 2018data reduction
Aimless0.6.2data scaling
PHASER2.8.1phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.24data extraction
xia20.5.580-g8b4a78df-dials-1.10data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QLP

1qlp


Resolution: 1.78→43.6 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2129 1904 5.11 %
Rwork0.1833 35320 -
obs0.1848 37224 99.8 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.31 Å2 / Biso mean: 53.0394 Å2 / Biso min: 23.79 Å2
Refinement stepCycle: final / Resolution: 1.78→43.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2812 0 28 195 3035
Biso mean--79.06 52.77 -
Num. residues----371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.82450.37281310.32924732604100
1.8245-1.87380.29891180.283625112629100
1.8738-1.9290.28631590.259624732632100
1.929-1.99120.26151640.231224762640100
1.9912-2.06240.25571180.212225222640100
2.0624-2.1450.25771390.205925212660100
2.145-2.24260.27651370.201525212658100
2.2426-2.36080.26531470.192724712618100
2.3608-2.50870.23761430.193425332676100
2.5087-2.70240.22151100.197425342644100
2.7024-2.97430.27541260.194325602686100
2.9743-3.40460.21771380.185625362674100
3.4046-4.28880.14831410.15625622703100
4.2888-43.61310.18531330.16232627276099
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)
14.4559-0.5526-0.44772.0111-0.10641.959-0.1183-0.09190.29880.22230.1758-0.1449-0.03860.3322-0.07730.26520.05920.00250.3189-0.05630.272324.4390.326516.696
23.0972-0.7512-1.85381.12051.03332.6601-0.0349-0.07430.0820.15250.09790.03320.15160.1747-0.0810.30740.060.00510.19210.03130.27047.7746-0.326927.5222
33.5011.33470.52366.1392-4.74684.4238-0.13530.6406-0.74260.14310.0476-0.4005-0.1489-0.13590.08851.26250.1579-0.16721.07760.11111.20177.6994-19.232535.9632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 174 )A24 - 174
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 394 )A175 - 394
3X-RAY DIFFRACTION3chain CC1

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