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- PDB-7aql: Crystal Structure of an Anti-Plasminogen Activator Inhibitor-1 (P... -

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Basic information

Entry
Database: PDB / ID: 7aql
TitleCrystal Structure of an Anti-Plasminogen Activator Inhibitor-1 (PAI-1) scFv antibody fragment (scFv-33H1F7)
ComponentsscFv-33H1F7
KeywordsIMMUNE SYSTEM / scFv / antibody fragment / immunoglobulin fold / PAI-1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSillen, M. / Weeks, S.D. / Strelkov, S.V. / Declerck, P.J.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)11ZQ918N Belgium
Research Foundation - Flanders (FWO)G072915N Belgium
CitationJournal: To Be Published
Title: Crystal Structure of an Anti-Plasminogen Activator Inhibitor-1 (PAI-1) scFv antibody fragment (scFv-33H1F7)
Authors: Sillen, M. / Weeks, S.D. / Strelkov, S.V. / Declerck, P.J.
History
DepositionOct 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: scFv-33H1F7
A: scFv-33H1F7
C: scFv-33H1F7
D: scFv-33H1F7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,56612
Polymers103,7984
Non-polymers7698
Water11,728651
1
B: scFv-33H1F7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1423
Polymers25,9491
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: scFv-33H1F7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1423
Polymers25,9491
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: scFv-33H1F7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1423
Polymers25,9491
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: scFv-33H1F7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1423
Polymers25,9491
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.398, 55.577, 102.493
Angle α, β, γ (deg.)90.000, 90.280, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

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Components

#1: Antibody
scFv-33H1F7


Mass: 25949.412 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pETHSUK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2(DE3)pLysS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.8 M DIAMMONIUM PHOSPHATE, 0.1 M BIS-TRIS, 4% w/v ACETONITRILE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.78→102.49 Å / Num. obs: 96894 / % possible obs: 93.9 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.026 / Rrim(I) all: 0.049 / Net I/σ(I): 14 / Num. measured all: 323744 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.78-1.883.30.56449945149280.7850.3610.6721.999.8
5.63-102.493.10.0271055833580.9980.0180.03234.198.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DZB

1dzb


Resolution: 1.8→45.21 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 2165 2.32 %
Rwork0.1857 91156 -
obs0.1866 93321 93.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.21 Å2 / Biso mean: 34.8309 Å2 / Biso min: 19.64 Å2
Refinement stepCycle: final / Resolution: 1.8→45.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7005 0 40 651 7696
Biso mean--48.28 40.09 -
Num. residues----904
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.34861450.295264056550100
1.84-1.890.33691600.249864246584100
1.89-1.940.2814920.23513530362255
1.94-20.26241370.209864116548100
2-2.060.2261430.202465066649100
2.06-2.130.27081470.20164106557100
2.13-2.220.24391710.198464306601100
2.22-2.320.2274970.19844070416763
2.32-2.440.21221800.201264306610100
2.44-2.60.26821370.20546467660499
2.6-2.80.23811240.209165006624100
2.8-3.080.25791790.20666449662899
3.08-3.520.23041500.18766432658299
3.52-4.440.18971550.14786069622493
4.44-45.210.17651480.16286623677198

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