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- PDB-6rod: Alpha-1-antitrypsin (Ser36Arg/Glu78Arg/Glu266Arg) in the native c... -

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Basic information

Entry
Database: PDB / ID: 6rod
TitleAlpha-1-antitrypsin (Ser36Arg/Glu78Arg/Glu266Arg) in the native conformation
ComponentsAlpha-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: 1.85 Å
AuthorsWan, M. / Ronzoni, R. / 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: Polymer accumulation in alpha-1 antitrypsin deficiency
Authors: Wan, M. / Ronzoni, R. / Irving, J.A. / Lomas, D.A.
History
DepositionMay 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: 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

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Assembly

Deposited unit
A: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)45,7381
Polymers45,7381
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.462, 38.958, 90.016
Angle α, β, γ (deg.)90.000, 103.910, 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: 45738.023 Da / Num. of mol.: 1 / Mutation: S36R, E78R, E266R
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 K-12 (bacteria) / Variant (production host): XL-1 Blue / References: UniProt: P01009
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.34 Å3/Da / Density % sol: 47.36 % / Description: Plate
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 22.5% PEG 1500, 0.1M SPG (succinate-phosphate-glycine) 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: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2019
Details: Oxford Danfysik/SESO Two stage demagnification using two K-B pairs of bimorph type mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.85→87.38 Å / Num. obs: 31051 / % possible obs: 93.1 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 15 / Num. measured all: 200390 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.896.81.1491362020140.7420.4771.2461.799.9
9.06-87.385.70.04518263190.9950.020.0534.398.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I7U

6i7u


Resolution: 1.85→43.688 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.95
RfactorNum. reflection% reflection
Rfree0.2231 1595 5.17 %
Rwork0.2013 --
obs0.2024 30872 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.89 Å2 / Biso mean: 42.7005 Å2 / Biso min: 18.15 Å2
Refinement stepCycle: final / Resolution: 1.85→43.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 0 182 2990
Biso mean---47.53 -
Num. residues----367
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8501-1.90980.39271490.35052436258595
1.9098-1.9780.34991410.31772063220499
1.978-2.05720.31591370.259628202957100
2.0572-2.15090.29181220.23162260238299
2.1509-2.26420.29361350.2492299243481
2.2642-2.40610.30541600.226228603020100
2.4061-2.59190.23711460.222128653011100
2.5919-2.85260.26591360.215828883024100
2.8526-3.26530.2121520.20829023054100
3.2653-4.11350.20311650.186328913056100
4.1135-43.70010.17031520.166129933145100

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