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- PDB-4pyw: 1.92 angstrom crystal structure of A1AT:TTAI ternary complex -

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Basic information

Entry
Database: PDB / ID: 4pyw
Title1.92 angstrom crystal structure of A1AT:TTAI ternary complex
Components
  • ACE-THR-THR-ALA-ILE-NH2
  • Alpha-1-antitrypsin
KeywordsHydrolase inhibitor / 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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsNyon, M.P. / Day, J. / Gooptu, B.
CitationJournal: Protein Sci. / Year: 2015
Title: An integrative approach combining ion mobility mass spectrometry, X-ray crystallography, and nuclear magnetic resonance spectroscopy to study the conformational dynamics of alpha 1 - ...Title: An integrative approach combining ion mobility mass spectrometry, X-ray crystallography, and nuclear magnetic resonance spectroscopy to study the conformational dynamics of alpha 1 -antitrypsin upon ligand binding.
Authors: Nyon, M.P. / Prentice, T. / Day, J. / Kirkpatrick, J. / Sivalingam, G.N. / Levy, G. / Haq, I. / Irving, J.A. / Lomas, D.A. / Christodoulou, J. / Gooptu, B. / Thalassinos, K.
History
DepositionMar 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1-antitrypsin
B: ACE-THR-THR-ALA-ILE-NH2
C: ACE-THR-THR-ALA-ILE-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6535
Polymers46,4693
Non-polymers1842
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-11 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.710, 38.960, 93.130
Angle α, β, γ (deg.)90.00, 100.13, 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 / Short peptide from AAT / SPAAT


Mass: 45611.742 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 / Plasmid: pQE32b / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: P01009
#2: Protein/peptide ACE-THR-THR-ALA-ILE-NH2


Mass: 428.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% PEG3350, 0.1 M Bis-Tris pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.0332 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.91→55.87 Å / Num. obs: 30573
Reflection shellResolution: 1.91→2.02 Å / Redundancy: 4 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 2.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→55.87 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.85 / SU B: 16.548 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.575 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22497 1518 5 %RANDOM
Rwork0.1904 ---
obs0.19219 28725 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.249 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å26.31 Å2
2---6.04 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.91→55.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 12 96 3045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193001
X-RAY DIFFRACTIONr_bond_other_d0.0010.022924
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9694054
X-RAY DIFFRACTIONr_angle_other_deg0.78736751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.985369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06525.649131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12915541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.855156
X-RAY DIFFRACTIONr_chiral_restr0.0810.2473
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213322
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02656
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_it4.1452.7141483
X-RAY DIFFRACTIONr_mcbond_other4.1462.7121482
X-RAY DIFFRACTIONr_mcangle_it5.1324.0511845
X-RAY DIFFRACTIONr_mcangle_other5.1314.0531846
X-RAY DIFFRACTIONr_scbond_it4.3943.2151518
X-RAY DIFFRACTIONr_scbond_other4.3923.2151518
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0394.5962208
X-RAY DIFFRACTIONr_long_range_B_refined5.86822.8463366
X-RAY DIFFRACTIONr_long_range_B_other5.8322.5453335
X-RAY DIFFRACTIONr_rigid_bond_restr2.76235925
X-RAY DIFFRACTIONr_sphericity_free39.127529
X-RAY DIFFRACTIONr_sphericity_bonded12.56355942
LS refinement shellResolution: 1.91→1.961 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 76 -
Rwork0.335 1647 -
obs--73.76 %
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)
12.8259-0.08-0.75360.21470.25790.8420.02310.85750.09080.10950.09160.03550.07180.1178-0.11480.14580.055-0.07780.70130.0280.224728.8122-13.3013-30.0714
23.4147-0.9360.48151.5965-1.05181.234-0.05250.5207-0.09710.13750.1266-0.22860.02990.0847-0.07410.06540.0864-0.07670.5872-0.04360.308144.9207-17.9206-24.1509
31.7118-0.0635-0.48690.28530.15480.6526-0.0040.2223-0.05280.0533-0.05420.01760.03260.0350.05820.20540.039-0.13190.4150.0030.294117.1143-15.5017-16.9444
42.0437-0.1365-0.62781.55880.31810.89910.04010.1574-0.06690.1304-0.0801-0.01380.08980.04740.03990.20190.023-0.11410.39560.04050.276313.4278-10.7795-11.3451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 123
2X-RAY DIFFRACTION2A124 - 185
3X-RAY DIFFRACTION3A186 - 342
4X-RAY DIFFRACTION4A343 - 393

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