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- PDB-4kds: Crystal structure of latent rainbow trout plasminogen activator i... -

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Basic information

Entry
Database: PDB / ID: 4kds
TitleCrystal structure of latent rainbow trout plasminogen activator inhibitor 1 (PAI-1)
ComponentsPlasminogen activator inhibitor 1
KeywordsHYDROLASE INHIBITOR / Serpin / Inactive serpin / trout uPA
Function / homology
Function and homology information


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
Plasminogen activator inhibitor 1
Similarity search - Component
Biological speciesOncorhynchus mykiss (rainbow trout)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6682 Å
AuthorsJohansen, J.S.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Protein conformational change delayed by steric hindrance from an N-linked glycan.
Authors: Bager, R. / Johansen, J.S. / Jensen, J.K. / Stensballe, A. / Jendroszek, A. / Buxbom, L. / Sorensen, H.P. / Andreasen, P.A.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasminogen activator inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1872
Polymers43,0911
Non-polymers961
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.065, 56.471, 59.750
Angle α, β, γ (deg.)90.00, 93.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Plasminogen activator inhibitor 1


Mass: 43091.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oncorhynchus mykiss (rainbow trout) / Gene: serpine1 / Production host: Escherichia coli (E. coli) / References: UniProt: I3WWD7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10 % PEG3350, 0.2M K-thiocyanate, 0.1M Hepes 7.0 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.039 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 13, 2013
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039 Å / Relative weight: 1
ReflectionResolution: 1.65→34.22 Å / Num. all: 46327 / Num. obs: 44752 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.3

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Processing

Software
NameVersionClassification
MAR345data collection
xia2data scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6682→20.219 Å / SU ML: 0.26 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 2255 5.04 %RANDOM
Rwork0.1725 ---
all0.1748 45054 --
obs0.1748 44707 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6682→20.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 5 399 3294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152968
X-RAY DIFFRACTIONf_angle_d1.6244015
X-RAY DIFFRACTIONf_dihedral_angle_d15.4711124
X-RAY DIFFRACTIONf_chiral_restr0.129454
X-RAY DIFFRACTIONf_plane_restr0.008522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6682-1.70440.41221390.36662483X-RAY DIFFRACTION93
1.7044-1.74410.3631360.34192616X-RAY DIFFRACTION99
1.7441-1.78760.3561530.29382631X-RAY DIFFRACTION99
1.7876-1.83590.34471330.25142622X-RAY DIFFRACTION99
1.8359-1.88990.26811290.21312681X-RAY DIFFRACTION99
1.8899-1.95090.26711260.1972640X-RAY DIFFRACTION99
1.9509-2.02060.23771310.1892679X-RAY DIFFRACTION100
2.0206-2.10140.21791480.18632640X-RAY DIFFRACTION100
2.1014-2.19690.20861290.15972665X-RAY DIFFRACTION100
2.1969-2.31260.23111420.16692690X-RAY DIFFRACTION100
2.3126-2.45720.20451480.17522650X-RAY DIFFRACTION100
2.4572-2.64660.24341330.17422687X-RAY DIFFRACTION100
2.6466-2.91220.22041420.17032665X-RAY DIFFRACTION100
2.9122-3.3320.19381590.16022682X-RAY DIFFRACTION100
3.332-4.19180.19281500.14062684X-RAY DIFFRACTION100
4.1918-20.22050.18571570.14762737X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -16.2005 Å / Origin y: -10.227 Å / Origin z: -20.8396 Å
111213212223313233
T0.147 Å20.0062 Å2-0.0334 Å2-0.149 Å20.0427 Å2--0.1487 Å2
L1.5634 °2-0.39 °2-0.6025 °2-1.08 °20.637 °2--0.9628 °2
S-0.0317 Å °-0.2202 Å °0.0571 Å °0.1226 Å °0.0809 Å °-0.0647 Å °0.0344 Å °0.0328 Å °-0.047 Å °
Refinement TLS groupSelection details: all

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