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- PDB-1d5s: CRYSTAL STRUCTURE OF CLEAVED ANTITRYPSIN POLYMER -

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Basic information

Entry
Database: PDB / ID: 1d5s
TitleCRYSTAL STRUCTURE OF CLEAVED ANTITRYPSIN POLYMER
Components(P1-ARG ANTITRYPSIN) x 2
KeywordsHYDROLASE INHIBITOR / SERPIN FOLD / RCL CLEAVAGE / A BETA SHEET POLYMERISATION
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
Serpins fold / Serpins 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 ...Serpins fold / Serpins 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 / Ribbon / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsDunstone, M.A. / Dai, W. / Whisstock, J.C. / Rossjohn, J. / Pike, R.N. / Feil, S.C. / Le Bonneic, B.F. / Parker, M.W. / Bottomley, S.P.
CitationJournal: Protein Sci. / Year: 2000
Title: Cleaved antitrypsin polymers at atomic resolution.
Authors: Dunstone, M.A. / Dai, W. / Whisstock, J.C. / Rossjohn, J. / Pike, R.N. / Feil, S.C. / Le Bonniec, B.F. / Parker, M.W. / Bottomley, S.P.
History
DepositionOct 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P1-ARG ANTITRYPSIN
B: P1-ARG ANTITRYPSIN


Theoretical massNumber of molelcules
Total (without water)42,3422
Polymers42,3422
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-41 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.170, 110.170, 76.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsEach neighbour in the polymer is oriented along the two-fold screw axis (crystallographic b axis) connected by the C-terminal fragment.

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Components

#1: Protein P1-ARG ANTITRYPSIN


Mass: 37634.793 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / Production host: Escherichia coli (E. coli) / References: UniProt: P01009
#2: Protein/peptide P1-ARG ANTITRYPSIN


Mass: 4707.596 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FRAGMENT / Mutation: M358R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: LIVER / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 4000 sodium citrate buffer t-butanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
220 %(w/v)PEG40001reservoir
30.1 Msodium citrate1reservoirpH5.5
42.5 %(v/v)t-butanol1reservoir

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 27, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 38524 / Num. obs: 9838 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 72.2 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.2
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.751 / % possible all: 98.4
Reflection
*PLUS
Num. measured all: 38524

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 3→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Each neighbour in the polymer is oriented along the two-fold screw axis (crystallographic b axis) connected by the C-terminal fragment.
RfactorNum. reflection
Rfree0.262 1614
Rwork0.208 -
all0.209 9782
obs0.209 8768
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 0 0 2984
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.208 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.09
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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