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- PDB-1qlp: 2.0 ANGSTROM STRUCTURE OF INTACT ALPHA-1-ANTITRYPSIN: A CANONICAL... -

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Basic information

Entry
Database: PDB / ID: 1qlp
Title2.0 ANGSTROM STRUCTURE OF INTACT ALPHA-1-ANTITRYPSIN: A CANONICAL TEMPLATE FOR ACTIVE SERPINS
ComponentsALPHA-1-ANTITRYPSINAlpha-1 antitrypsin
KeywordsSERINE PROTEASE INHIBITOR / SERPIN / GLYCOPROTEIN / POLYMORPHISM / EMPHYSEMA / DISEASE MUTATION / ACUTE PHASE
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 / Resolution: 2 Å
AuthorsElliott, P.R. / Pei, X.Y. / Dafforn, T. / Read, R.J. / Carrell, R.W. / Lomas, D.A.
Citation
Journal: Protein Sci. / Year: 2000
Title: Topography of a 2.0 A structure of alpha1-antitrypsin reveals targets for rational drug design to prevent conformational disease.
Authors: Elliott, P.R. / Pei, X.Y. / Dafforn, T.R. / Lomas, D.A.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Wildtype Alpha1-Antitrypsin is in the Canonical Inhibitory Conformation
Authors: Elliott, P.R. / Abrahams, J.-P. / Lomas, D.A.
History
DepositionSep 10, 1999Deposition site: PDBE / Processing site: PDBE
SupersessionSep 27, 1999ID: 2PSI
Revision 1.0Sep 27, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4Oct 9, 2019Group: Data collection / Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.status_code_sf
Revision 1.5Dec 13, 2023Group: 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)44,3801
Polymers44,3801
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.680, 39.260, 90.270
Angle α, β, γ (deg.)90.00, 104.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ALPHA-1-ANTITRYPSIN / Alpha-1 antitrypsin / ALPHA-1-PROTEINASE INHIBITOR / ALPHA-1-ANTIPROTEINASE


Mass: 44380.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: HEPATOCYTES / Cell: NEUTROPHILS / Cellular location: CYTOPLASM / Gene: ALPHA-1-ANTITRYPSIN / Organ: LIVER / Plasmid: PTERMAT / Gene (production host): ALPHA-1-ANTITRYPSIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01009
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.6 Å3/Da / Density % sol: 37.2 %
Description: DATA WERE COLLECTED USING THE OSCILLATION METHOD.
Crystal growpH: 6
Details: 24% PEG 4000, 0.2 M SODIUM ACETATE, 0.1M TRIS-HCL PH 6.0, 2MM FESO4.7H20
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
124 %(w/v)PEG40001reservoir
20.2 M1reservoirNaOAc
30.1 MTris-HCl1reservoirpH6.0
42 mM1reservoirFeSO4-7H2O

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 9, 1998 / Details: MIRRORS
RadiationMonochromator: BENT CYLINDRICAL GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 25057 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 29.41 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.067 / Net I/σ(I): 5.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.415 / % possible all: 95.2
Reflection
*PLUS
Num. measured all: 156306
Reflection shell
*PLUS
Redundancy: 2.2 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
CNS0.5refinement
MOSFLMdata reduction
SCALAdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THERMOSTABLE VARIANT ALPHA1-ANTITRYPSIN (PDB ENTRY 1PSI)

1psi


Resolution: 2→25 Å / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R-VALUE / σ(F): 0
Details: THE N-TERMINAL RESIDUES 1-22 WERE NOT OBSERVED IN THE ELECTRON DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1271 4.7 %RANDOM
Rwork0.231 ---
obs0.231 25039 93.6 %-
Solvent computationSolvent model: CNS / Bsol: 215 Å2 / ksol: 1.257 e/Å3
Displacement parametersBiso mean: 38.38 Å2
Baniso -1Baniso -2Baniso -3
1--4.094 Å20 Å2-6.005 Å2
2--0.601 Å20 Å2
3---3.493 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-0 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 0 106 3062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006917
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.30665
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.95182
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.23128
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.5021.5
X-RAY DIFFRACTIONc_mcangle_it4.7322
X-RAY DIFFRACTIONc_scbond_it2.2192
X-RAY DIFFRACTIONc_scangle_it3.4532.5
LS refinement shellResolution: 2→2.07 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.334 96 4.7 %
Rwork0.297 1837 -
obs--72.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:WATER_REP.PARAM
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006917
X-RAY DIFFRACTIONc_angle_deg1.30665
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.95182
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.23128

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