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- PDB-1sek: THE STRUCTURE OF ACTIVE SERPIN K FROM MANDUCA SEXTA AND A MODEL F... -

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Basic information

Entry
Database: PDB / ID: 1sek
TitleTHE STRUCTURE OF ACTIVE SERPIN K FROM MANDUCA SEXTA AND A MODEL FOR SERPIN-PROTEASE COMPLEX FORMATION
ComponentsSERPIN K
KeywordsSERINE PROTEASE INHIBITOR / SERPIN / PROTEASE
Function / homology
Function and homology information


response to bacterium / serine-type endopeptidase inhibitor activity / extracellular space
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
Alaserpin / Serine protease inhibitor
Similarity search - Component
Biological speciesManduca sexta (tobacco hornworm)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsLi, J. / Wang, Z. / Canagarajah, B. / Jiang, H. / Kanost, M. / Goldsmith, E.J.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The structure of active serpin 1K from Manduca sexta.
Authors: Li, J. / Wang, Z. / Canagarajah, B. / Jiang, H. / Kanost, M. / Goldsmith, E.J.
History
DepositionMar 6, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERPIN K


Theoretical massNumber of molelcules
Total (without water)42,2731
Polymers42,2731
Non-polymers00
Water2,072115
1
A: SERPIN K

A: SERPIN K


Theoretical massNumber of molelcules
Total (without water)84,5462
Polymers84,5462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)125.960, 42.050, 76.050
Angle α, β, γ (deg.)90.00, 117.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SERPIN K


Mass: 42273.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Tissue: HEMOLYMPH / Cellular location: EXTRACELLULAR / Plasmid: H6PQE-60 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P14754, UniProt: Q25526*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 35 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 5.8 / Method: vapor diffusion
Details: drop contains equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
228 %PEG60001reservoir
31.2 M1reservoirNH4Cl
41 mMEDTA1reservoir
55 mMdithiothreitol1reservoir
6100 mMMES1reservoir

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Data collection

RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 20609 / % possible obs: 93.9 % / Redundancy: 2 % / Num. measured all: 43967 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 66 % / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
X-PLOR3.85phasing
RefinementResolution: 2.1→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2040 10 %RANDOM
Rwork0.199 ---
obs0.199 22036 90.5 %-
Displacement parametersBiso mean: 31.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 0 114 3187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 207 12 %
Rwork0.294 1743 -
obs--66 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPH19.PEP
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Version: 3.85 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 20404
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.4
X-RAY DIFFRACTIONx_angle_deg
LS refinement shell
*PLUS
Rfactor obs: 0.294

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