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- PDB-1qmb: Cleaved alpha-1-antitrypsin polymer -

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Basic information

Entry
Database: PDB / ID: 1qmb
TitleCleaved alpha-1-antitrypsin polymer
Components(ALPHA-1-ANTITRYPSIN) x 2
KeywordsSERINE PROTEASE INHIBITOR / SERPIN / ANTITRYPSIN / POLYMER / CLEAVED
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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHuntington, J.A. / Pannu, N.S. / Hazes, B. / Read, R.J. / Lomas, D.A. / Carrell, R.W.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: A 2.6A Structure of a Serpin Polymer and Implications for Conformational Disease
Authors: Huntington, J.A. / Pannu, N.S. / Hazes, B. / Read, R.J. / Lomas, D.A. / Carrell, R.W.
History
DepositionSep 24, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)41,3862
Polymers41,3862
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-51.6 kcal/mol
Surface area19810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)108.590, 108.590, 110.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein ALPHA-1-ANTITRYPSIN / ALPHA-1-PROTEINASE INHIBITOR / ALPHA-1-PI


Mass: 36623.742 Da / Num. of mol.: 1 / Fragment: RESIDUES 49-69,71-302,304-376 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01009
#2: Protein/peptide ALPHA-1-ANTITRYPSIN / ALPHA-1-PROTEINASE INHIBITOR / ALPHA-1-PI


Mass: 4762.651 Da / Num. of mol.: 1 / Fragment: RESIDUES 377-418 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01009
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCRYSTAL TRIALS WERE SET UP FOR S195A THROMBIN AND M358R ALPHA-1-ANTITRYPSIN. THE CRYSTALS CONTAINED ...CRYSTAL TRIALS WERE SET UP FOR S195A THROMBIN AND M358R ALPHA-1-ANTITRYPSIN. THE CRYSTALS CONTAINED ONLY P7-P6 CLEAVED ALPHA-1-ANTITRYPSIN AND THE REMAINING MOTHERLIQOUR WAS PREDOMINANTLY S195A THROMBIN.
Sequence detailsPREVIOUSLY UNIDENTIFIED CLEAVAGE SITE CHAIN BREAK SER 45 A --- SER 47 A MISSING RESIDUE ASN 46 A ...PREVIOUSLY UNIDENTIFIED CLEAVAGE SITE CHAIN BREAK SER 45 A --- SER 47 A MISSING RESIDUE ASN 46 A CHAIN BREAK ASN 278 A --- ASP 280 A MISSING RESIDUE GLU 279 A

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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: 4.46 Å3/Da / Density % sol: 73 %
Description: MOLECULAR REPLACEMENT WAS CONDUCTED IN THE ABSENCE OF S4A
Crystal growpH: 8.5
Details: 0.2M TRI-SODIUM CITRATE, 0.1M TRIS, PH 8.5, 30% PEG 400
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %(w/v)PEG40011
2200 mM11NaCl
3100 mMTris-HCl11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.9
DetectorType: ADSC QUANTUM / Detector: CCD / Date: May 15, 1999 / Details: MIRRORS
RadiationMonochromator: SI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.57→27.27 Å / Num. obs: 17423 / % possible obs: 71.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.209 / Rsym value: 0.183 / Net I/σ(I): 13.73
Reflection shellResolution: 2.57→2.71 Å / Redundancy: 1.6 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.3 / Rsym value: 1 / % possible all: 12.5
Reflection shell
*PLUS
% possible obs: 12.5 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
MOSFLMdata reduction
SCALAdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ETRY 7API

7api


Resolution: 2.6→27.27 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1038103.31 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 875 5 %RANDOM
Rwork0.212 ---
obs0.212 17423 73.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9487 Å2 / ksol: 0.321472 e/Å3
Displacement parametersBiso mean: 69.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-4.68 Å20 Å2
2--0.06 Å20 Å2
3----0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.81 Å
Refinement stepCycle: LAST / Resolution: 2.6→27.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 0 17 2890
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.59
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it41.5
X-RAY DIFFRACTIONc_mcangle_it6.252
X-RAY DIFFRACTIONc_scbond_it8.742
X-RAY DIFFRACTIONc_scangle_it11.862.5
LS refinement shellResolution: 2.57→2.73 Å / Rfactor Rfree error: 0.073 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 26 4.9 %
Rwork0.409 501 -
obs--13.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.59

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