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- PDB-1by7: HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2. LOOP (66-98) DELETION MUTANT -

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Basic information

Entry
Database: PDB / ID: 1by7
TitleHUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2. LOOP (66-98) DELETION MUTANT
ComponentsPROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-2)
KeywordsPROTEIN BINDING / SERPIN
Function / homology
Function and homology information


cornified envelope / Dissolution of Fibrin Clot / fibrinolysis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / serine-type endopeptidase inhibitor activity / negative regulation of apoptotic process / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Plasminogen activator inhibitor-2 / 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 ...Plasminogen activator inhibitor-2 / 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
Plasminogen activator inhibitor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsHarrop, S.J. / King, G.C. / Mabbutt, B.C. / Curmi, P.M.G.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The crystal structure of plasminogen activator inhibitor 2 at 2.0 A resolution: implications for serpin function.
Authors: Harrop, S.J. / Jankova, L. / Coles, M. / Jardine, D. / Whittaker, J.S. / Gould, A.R. / Meister, A. / King, G.C. / Mabbutt, B.C. / Curmi, P.M.
History
DepositionOct 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-2)


Theoretical massNumber of molelcules
Total (without water)43,0451
Polymers43,0451
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.820, 41.730, 77.400
Angle α, β, γ (deg.)90.00, 114.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-2) / PAI-2


Mass: 43045.020 Da / Num. of mol.: 1 / Mutation: RESIDUES 66 - 98 EXCISED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05120
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
215 %PEG80001reservoir
30.12 Mmagnesium acetate1reservoir
40.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 27274 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.35 / Rsym value: 0.35 / % possible all: 98
Reflection
*PLUS
Num. measured all: 176011
Reflection shell
*PLUS
% possible obs: 90.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: MIR / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1360 5 %RANDOM
Rwork0.202 ---
obs-27274 99 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2836 0 0 209 3045
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.04

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