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- PDB-1psi: Intact recombined alpha1-antitrypsin mutant PHE 51 to LEU -

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Basic information

Entry
Database: PDB / ID: 1psi
TitleIntact recombined alpha1-antitrypsin mutant PHE 51 to LEU
ComponentsALPHA=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-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / 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-coated ER to Golgi transport vesicle / COPII-mediated vesicle transport / 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 / ficolin-1-rich granule lumen / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum / Golgi apparatus / 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 / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsAbrahams, J.P. / Elliott, P.R. / Lomas, D.A. / Carrell, R.W.
CitationJournal: Nat.Struct.Biol. / Year: 1996
Title: Inhibitory conformation of the reactive loop of alpha 1-antitrypsin.
Authors: Elliott, P.R. / Lomas, D.A. / Carrell, R.W. / Abrahams, J.P.
History
DepositionJun 11, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA=1=-ANTITRYPSIN


Theoretical massNumber of molelcules
Total (without water)44,4071
Polymers44,4071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.958, 38.508, 88.928
Angle α, β, γ (deg.)90.00, 104.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ALPHA=1=-ANTITRYPSIN


Mass: 44406.539 Da / Num. of mol.: 1 / Mutation: F51L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD PLASMA / Gene: ALPHA-1-ANTITRYPSIN / Organ: BLOOD / Plasmid: PTERMAT / Gene (production host): ALPHA-1-ANTITRYPSIN / Production host: Escherichia coli (E. coli) / 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: 2.11 Å3/Da / Density % sol: 45 %
Crystal growpH: 6
Details: 24% PEG, 0.2 M SODIUM ACETATE, 0.1 M TRIS.HCL, PH 6.0, 0.002 M FESO4, 25 DEG CELSIUS
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: ROTATING ANODE / Type: ELLIOTT GX-11 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 12, 1996 / Details: NICKEL COATED DOUBLE MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.92→19.5 Å / Num. obs: 7651 / % possible obs: 91.7 % / Observed criterion σ(I): 3.5 / Redundancy: 2.2 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 8.36
Reflection shellResolution: 2.91→3.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 4 / Rsym value: 0.204 / % possible all: 74.4
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 6 Å / Rmerge(I) obs: 0.114
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3.1 Å / % possible obs: 74.4 % / Rmerge(I) obs: 0.204

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CLEAVED ALPHA1-ANTITRYPSIN (PDB ENTRY 9API)

9api


Resolution: 2.92→6 Å / σ(F): 0
Details: RESIDUES 106 - 108 ARE POORLY ORDERED. ALTHOUGH SOME CONNECTED DENSITY EXISTS, A STEREOCHEMICALLY CORRECT MODEL FITTING THE DATA COULD NOT BE BUILT. THE OCCUPANCIES OF THESE RESIDUES ARE SET ...Details: RESIDUES 106 - 108 ARE POORLY ORDERED. ALTHOUGH SOME CONNECTED DENSITY EXISTS, A STEREOCHEMICALLY CORRECT MODEL FITTING THE DATA COULD NOT BE BUILT. THE OCCUPANCIES OF THESE RESIDUES ARE SET TO ZERO. PRO 106 - SER 108 IS A POORLY ORDERED LOOP, PRESENT IN MULTIPLE CONFORMATIONS. A STEREOCHEMICALLY VALID MODEL WAS BUILT, BUT THE OCCUPANCIES ARE SET TO ZERO.
RfactorNum. reflection% reflection
Rfree0.288 --
Rwork0.218 --
obs0.218 6699 91.7 %
Refinement stepCycle: LAST / Resolution: 2.92→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2956 0 0 0 2956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.53
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d15.76
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: 'TNT and X-PLOR' / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.218 / Rfactor Rfree: 0.288 / Rfactor Rwork: 0.215 / Highest resolution: 2.9 Å / Num. reflection all: 6699 / Num. reflection Rfree: 754
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg15.761
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg
X-RAY DIFFRACTIONt_bond_d0.0065
X-RAY DIFFRACTIONt_angle_deg1.27
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_improper_angle_deg
X-RAY DIFFRACTIONt_planar_d0.0052
X-RAY DIFFRACTIONt_plane_restr0.0075

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