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- PDB-3dru: Crystal Structure of Gly117Phe Alpha1-Antitrypsin -

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Basic information

Entry
Database: PDB / ID: 3dru
TitleCrystal Structure of Gly117Phe Alpha1-Antitrypsin
ComponentsAlpha-1-antitrypsin
KeywordsHydrolase inhibitor / serpin / serine proteinase inhibitor / alpha1-antitrypsin / polymerisation / rational drug design / conformational disease / emphysema / cirrhosis / Acute phase / Alternative splicing / Blood coagulation / Disease mutation / Glycoprotein / Hydrolase / Polymorphism / Protease / Protease inhibitor / Secreted / Serine protease inhibitor
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 / Resolution: 3.2 Å
AuthorsGooptu, B. / Nobeli, I. / Purkiss, A. / Phillips, R.L. / Mallya, M. / Lomas, D.A. / Barrett, T.E.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystallographic and cellular characterisation of two mechanisms stabilising the native fold of alpha1-antitrypsin: implications for disease and drug design.
Authors: Gooptu, B. / Miranda, E. / Nobeli, I. / Mallya, M. / Purkiss, A. / Brown, S.C. / Summers, C. / Phillips, R.L. / Lomas, D.A. / Barrett, T.E.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-1-antitrypsin
B: Alpha-1-antitrypsin
C: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)137,1063
Polymers137,1063
Non-polymers00
Water00
1
A: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)45,7021
Polymers45,7021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)45,7021
Polymers45,7021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Alpha-1-antitrypsin


Theoretical massNumber of molelcules
Total (without water)45,7021
Polymers45,7021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.840, 149.300, 77.290
Angle α, β, γ (deg.)90.000, 94.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-1-antitrypsin / Alpha-1 protease inhibitor / Alpha-1-antiproteinase


Mass: 45701.867 Da / Num. of mol.: 3 / Mutation: G117F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA1, AAT, PI, PRO0684, PRO2209 / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1Blue / References: UniProt: P01009

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Li2SO4, Tris/HCl, pH 8.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 3→77.152 Å / Num. obs: 26618 / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.155 / Rsym value: 0.155 / Net I/σ(I): 3.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.164.80.9350.81853538870.93599.8
3.16-3.354.80.6131.21764336800.61399.8
3.35-3.594.80.36521638334330.36599.7
3.59-3.874.80.24331524432090.24399.7
3.87-4.244.70.1741398229540.1799.7
4.24-4.744.70.1165.41256726630.11699.7
4.74-5.484.70.1055.91104123660.10599.8
5.48-6.714.60.1135.5930520150.11399.8
6.71-9.494.40.0776.8678415380.07798.8
9.49-149.34.50.0757.439238730.075100

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 3.2→55 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.29 1116 5.1 %
Rwork0.242 --
obs-21915 99.6 %
Solvent computationBsol: 32.527 Å2
Displacement parametersBiso max: 149.39 Å2 / Biso mean: 68.872 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-28.741 Å20 Å222.848 Å2
2--2.295 Å20 Å2
3----31.036 Å2
Refinement stepCycle: LAST / Resolution: 3.2→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8560 0 0 0 8560
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.627
X-RAY DIFFRACTIONc_mcbond_it1.9541.5
X-RAY DIFFRACTIONc_scbond_it2.1832
X-RAY DIFFRACTIONc_mcangle_it3.3652
X-RAY DIFFRACTIONc_scangle_it3.6792.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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