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- PDB-5nbv: Crystal structure of native alpha-1-antitrypsin with seven stabil... -

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Basic information

Entry
Database: PDB / ID: 5nbv
TitleCrystal structure of native alpha-1-antitrypsin with seven stabilising mutations
ComponentsAlpha-1-antitrypsin
KeywordsHYDROLASE / SERPIN
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 / collagen-containing extracellular matrix / 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 / Resolution: 1.73 Å
AuthorsHuntington, J.A. / Pomowski, A. / Johnson, D.J.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/L017431/1 United Kingdom
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF THE Z VARIANT OF ALPHA-1-ANTITRYPSIN REVEALS STRUCTURAL AND DYNAMICAL CHANGES AND SUPPORTS A C-TERMINAL DOMAIN SWAP MECHANISM OF POLYMERIZATION
Authors: Johnson, D.J.D. / Pomowski, A. / Huntington, J.A.
History
DepositionMar 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6174
Polymers42,3401
Non-polymers2763
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-1 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.700, 39.260, 90.560
Angle α, β, γ (deg.)90.00, 104.08, 90.00
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: 42340.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Production host: Escherichia coli (E. coli) / References: UniProt: P01009
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, carboxylic acid mixture

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.73→52.85 Å / Num. obs: 40844 / % possible obs: 99.8 % / Redundancy: 3.1 % / Net I/σ(I): 7.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NBU

5nbu


Resolution: 1.73→52.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.654 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25931 2056 5 %RANDOM
Rwork0.21645 ---
obs0.21865 38771 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.987 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å21.4 Å2
2---0.4 Å20 Å2
3---0.52 Å2
Refinement stepCycle: 1 / Resolution: 1.73→52.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2789 0 18 200 3007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0192989
X-RAY DIFFRACTIONr_bond_other_d00.022816
X-RAY DIFFRACTIONr_angle_refined_deg0.5811.974071
X-RAY DIFFRACTIONr_angle_other_deg0.45636463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.4925391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10825.424118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46115473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.095155
X-RAY DIFFRACTIONr_chiral_restr0.0440.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213421
X-RAY DIFFRACTIONr_gen_planes_other00.02658
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0463.3761552
X-RAY DIFFRACTIONr_mcbond_other4.0413.3731551
X-RAY DIFFRACTIONr_mcangle_it5.4285.031947
X-RAY DIFFRACTIONr_mcangle_other5.4275.0321948
X-RAY DIFFRACTIONr_scbond_it4.7173.681437
X-RAY DIFFRACTIONr_scbond_other4.7163.681437
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6615.382125
X-RAY DIFFRACTIONr_long_range_B_refined8.43340.5393196
X-RAY DIFFRACTIONr_long_range_B_other8.43340.5553197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 160 -
Rwork0.37 2845 -
obs--99.5 %

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