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- PDB-8ol9: Anti-FIXa Fab in complex with human des-(Gla-EGF1) FIXa -

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Basic information

Entry
Database: PDB / ID: 8ol9
TitleAnti-FIXa Fab in complex with human des-(Gla-EGF1) FIXa
Components
  • (Coagulation factor IX ...) x 2
  • Heavy chain of FIXa binding Fab
  • Light chain of FIXa binding Fab
KeywordsBLOOD CLOTTING / Fab / FIXa
Function / homology
Function and homology information


Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation ...Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Golgi lumen / blood coagulation / collagen-containing extracellular matrix / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-0GJ / Coagulation factor IX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJohansson, E. / Svensson, L.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2023
Title: Computational design of N-linked glycans for high throughput epitope profiling.
Authors: Greisen, P.J. / Yi, L. / Zhou, R. / Zhou, J. / Johansson, E. / Dong, T. / Liu, H. / Johnsen, L.B. / Lund, S. / Svensson, L.A. / Zhu, H. / Thomas, N. / Yang, Z. / Ostergaard, H.
History
DepositionMar 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation_author.name
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light chain of FIXa binding Fab
B: Heavy chain of FIXa binding Fab
H: Coagulation factor IX heavy chain
L: Coagulation factor IX light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9039
Polymers80,1534
Non-polymers7505
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-83 kcal/mol
Surface area31950 Å2
Unit cell
Length a, b, c (Å)61.440, 97.270, 366.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Coagulation factor IX ... , 2 types, 2 molecules HL

#3: Protein Coagulation factor IX heavy chain / Christmas factor / Plasma thromboplastin component / PTC


Mass: 26190.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Coagulation factor IX - Homo sapiens / Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli (E. coli) / References: UniProt: P00740, coagulation factor IXa
#4: Protein Coagulation factor IX light chain / Christmas factor / Plasma thromboplastin component / PTC


Mass: 6470.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli (E. coli) / References: UniProt: P00740, coagulation factor IXa

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Antibody , 2 types, 2 molecules AB

#1: Antibody Light chain of FIXa binding Fab


Mass: 23461.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Heavy chain of FIXa binding Fab


Mass: 24030.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 42 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-0GJ / L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide


Type: peptide-like / Mass: 395.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28ClN6O5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5 M ammonium sulphate, 0.1 M sodium citrate, pH 5.6, !.0 M lithium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→49.98 Å / Num. obs: 33502 / % possible obs: 96.24 % / Redundancy: 4.8 % / Biso Wilson estimate: 50.02 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1322 / Rpim(I) all: 0.06544 / Rrim(I) all: 0.148 / Net I/σ(I): 10.62
Reflection shellResolution: 2.602→2.695 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 2497 / CC1/2: 0.69 / CC star: 0.904 / Rpim(I) all: 0.452 / Rrim(I) all: 0.9306 / % possible all: 73.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.98 Å / SU ML: 0.4194 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.8441
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3233 1657 5 %
Rwork0.2666 31483 -
obs0.2695 33140 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5559 0 45 37 5641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035758
X-RAY DIFFRACTIONf_angle_d0.55217811
X-RAY DIFFRACTIONf_chiral_restr0.0433858
X-RAY DIFFRACTIONf_plane_restr0.00351002
X-RAY DIFFRACTIONf_dihedral_angle_d4.3368797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.680.4686970.36441855X-RAY DIFFRACTION68.68
2.68-2.770.35161400.32722646X-RAY DIFFRACTION99.61
2.77-2.860.37071410.31472683X-RAY DIFFRACTION99.37
2.86-2.980.41881390.33682650X-RAY DIFFRACTION99.82
2.98-3.110.39031420.31222716X-RAY DIFFRACTION99.79
3.11-3.280.38691420.30212673X-RAY DIFFRACTION99.54
3.28-3.480.32721420.29452711X-RAY DIFFRACTION99.83
3.48-3.750.42961340.35332530X-RAY DIFFRACTION93.61
3.75-4.130.31361370.2562612X-RAY DIFFRACTION95.29
4.13-4.730.25321430.19832733X-RAY DIFFRACTION99.76
4.73-5.950.23691450.20522757X-RAY DIFFRACTION99.66
5.95-49.980.27421550.22662917X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -25.9522906073 Å / Origin y: -26.166444968 Å / Origin z: -56.609126574 Å
111213212223313233
T0.379843252529 Å2-0.0465753763153 Å2-0.0130054145799 Å2-0.304258676334 Å2-0.0208925811772 Å2--0.24254655289 Å2
L0.589799284109 °2-0.0634405567773 °2-0.0376269424582 °2-0.417107282203 °2-0.0941764353053 °2--0.692744593877 °2
S0.0663470563187 Å °-0.297090534127 Å °0.0182854428965 Å °0.361589766343 Å °0.0524394121416 Å °-0.0309993196652 Å °-0.0873130888483 Å °0.00916821642947 Å °-0.0734513767801 Å °
Refinement TLS groupSelection details: all

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