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- PDB-4dte: Crystal structure of zebrafish plasminogen activator inhibitor-1 ... -

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Basic information

Entry
Database: PDB / ID: 4dte
TitleCrystal structure of zebrafish plasminogen activator inhibitor-1 (PAI-1)
ComponentsSerpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
KeywordsHYDROLASE INHIBITOR / Active serpin / zebarfish uPA
Function / homology
Function and homology information


ECM proteoglycans / : / Platelet degranulation / negative regulation of endopeptidase activity / negative regulation of plasminogen activation / 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 speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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
DepositionFeb 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Other
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Aug 14, 2013Group: Database references
Revision 1.4Aug 21, 2013Group: Database references / Structure summary
Revision 1.5Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
B: Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5144
Polymers84,0722
Non-polymers4422
Water7,981443
1
A: Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2572
Polymers42,0361
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2572
Polymers42,0361
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.160, 73.770, 91.750
Angle α, β, γ (deg.)90.00, 102.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1


Mass: 42035.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: serpine1
Cell line (production host): HUMAN EMBRYONIC KIDNEY CELLS (HEK-293)
Cellular location (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: F1QRB8
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 6.1
Details: 20% (w/v) PEG3350, 0.2 M NaCl, 0.1 M bis-Tris, pH 6.1, VAPOR DIFFUSION, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.96→59.15 Å / Num. all: 61074 / Num. obs: 60335 / % possible obs: 98.8 % / Observed criterion σ(I): 11.98
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.96-2.01195.5
2-2.07199.6
2.08-2.13199.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
xia2IIdata reduction
xia2IIdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3Q02
Resolution: 1.96→44.747 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 23.58 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2189 2000 3.32 %
Rwork0.1736 --
obs0.1751 60303 98.83 %
all-61074 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7527 Å20 Å25.2108 Å2
2---1.9212 Å20 Å2
3---6.6739 Å2
Refinement stepCycle: LAST / Resolution: 1.96→44.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5822 0 28 443 6293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195963
X-RAY DIFFRACTIONf_angle_d1.7578049
X-RAY DIFFRACTIONf_dihedral_angle_d16.0872253
X-RAY DIFFRACTIONf_chiral_restr0.131909
X-RAY DIFFRACTIONf_plane_restr0.0091038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9601-2.00910.32171380.26324014X-RAY DIFFRACTION96
2.0091-2.06340.31841430.25644155X-RAY DIFFRACTION100
2.0634-2.12410.30431430.244187X-RAY DIFFRACTION100
2.1241-2.19270.29021430.23034172X-RAY DIFFRACTION99
2.1927-2.2710.30561420.21284151X-RAY DIFFRACTION99
2.271-2.3620.29081430.20144150X-RAY DIFFRACTION99
2.362-2.46940.23911430.19564171X-RAY DIFFRACTION99
2.4694-2.59960.21911420.18634163X-RAY DIFFRACTION99
2.5996-2.76250.22811430.18164163X-RAY DIFFRACTION99
2.7625-2.97570.22751430.17464164X-RAY DIFFRACTION99
2.9757-3.27510.21061430.17064185X-RAY DIFFRACTION99
3.2751-3.74880.19891440.15244171X-RAY DIFFRACTION99
3.7488-4.72230.18561440.13484218X-RAY DIFFRACTION99
4.7223-44.7590.16771460.1544239X-RAY DIFFRACTION98

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