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- PDB-5jb8: Crystal structure of factor IXa variant K98T in complex with EGR-... -

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Basic information

Entry
Database: PDB / ID: 5jb8
TitleCrystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone
Components(Coagulation factor ...) x 2
KeywordsHYDROLASE / BLOOD CLOTTING / GLYCOPROTEIN / HAEMOSTASIS
Function / homology
Function and homology information


Defective F9 secretion / coagulation factor IXa / Defective gamma-carboxylation of F9 / 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 / coagulation factor IXa / Defective gamma-carboxylation of F9 / 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 / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Golgi lumen / blood coagulation / : / 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 / Laminin / Laminin / 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. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / 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 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GLU-GLY-ARG-CHLOROMETHYL KETONE / Chem-0GJ / Coagulation factor IX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsKristensen, L.H. / Brandstetter, H.
CitationJournal: Biochem.J. / Year: 2016
Title: Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site.
Authors: Kristensen, L.H. / Olsen, O.H. / Blouse, G.E. / Brandstetter, H.
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Non-polymer description
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
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
E: Coagulation factor IX
S: Coagulation factor IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0725
Polymers32,5582
Non-polymers5143
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-20 kcal/mol
Surface area13630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.230, 67.140, 96.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Coagulation factor ... , 2 types, 2 molecules ES

#1: Protein Coagulation factor IX / Christmas factor / Plasma thromboplastin component / PTC


Mass: 6395.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fragment: EGF2 DOMAIN, RESIDUES 133-191 / Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): NiCo21 / References: UniProt: P00740, coagulation factor IXa
#2: Protein Coagulation factor IX / Christmas factor / Plasma thromboplastin component / PTC


Mass: 26162.742 Da / Num. of mol.: 1 / Mutation: K98T
Source method: isolated from a genetically manipulated source
Details: Fragment: CATALYTIC DOMAIN, RESIDUES 227-461 / Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Nico21 / References: UniProt: P00740, coagulation factor IXa

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Non-polymers , 4 types, 257 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


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


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 395.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28ClN6O5 / References: GLU-GLY-ARG-CHLOROMETHYL KETONE
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 18-20% PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 7, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.45→16.77 Å / Num. all: 228593 / Num. obs: 51455 / % possible obs: 99.15 % / Redundancy: 4.4 % / Biso Wilson estimate: 19.46 Å2 / Rmerge(I) obs: 0.08072 / Net I/σ(I): 7.22
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.7014 / Mean I/σ(I) obs: 1.8 / % possible all: 98.97

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
iMOSFLM7.1.1data reduction
Aimless0.3.11data scaling
MOLREP11.2.08phasing
REFMAC5.8.0073refinement
Coot0.8.1-premodel building
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wph

1wph
PDB Unreleased entry


Resolution: 1.45→16.77 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.05
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 2504 4.88 %HKL reflections copied from pdb entry 2wph
Rwork0.1516 ---
obs0.1532 51350 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.3 Å2 / Biso mean: 32.3 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 1.45→16.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 56 256 2537
Biso mean--29.18 38.93 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142342
X-RAY DIFFRACTIONf_angle_d1.5463150
X-RAY DIFFRACTIONf_chiral_restr0.092344
X-RAY DIFFRACTIONf_plane_restr0.009409
X-RAY DIFFRACTIONf_dihedral_angle_d14.992838
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.47790.31711250.28682705283098
1.4779-1.5080.26321180.26492641275998
1.508-1.54080.27161350.24732655279098
1.5408-1.57660.26171510.21422628277997
1.5766-1.6160.23481460.20562654280098
1.616-1.65970.20451180.19392662278098
1.6597-1.70850.24321450.18242705285099
1.7085-1.76350.21791220.17392667278999
1.7635-1.82650.22291260.1682729285599
1.8265-1.89950.19961480.169126912839100
1.8995-1.98590.18321240.158927482872100
1.9859-2.09040.18061550.148227172872100
2.0904-2.22110.16181410.147627472888100
2.2211-2.39210.17391520.1442691284399
2.3921-2.6320.17861550.1472727288299
2.632-3.0110.17161450.15062743288899
3.011-3.78630.19271560.134727872943100
3.7863-16.77590.15471420.125829493091100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
12.0599-1.2974-0.23723.1037-0.82611.8309-0.5985-0.737-0.13880.99180.5523-0.0681-0.0634-0.360.04060.51110.1546-0.00330.4164-0.00230.2113Chain E, EGF2 domain-6.3803-21.109440.0735
22.5347-0.4774-0.04051.89480.24361.152-0.0752-0.0816-0.0876-0.04110.0320.03760.1158-0.01060.03830.1255-0.0008-0.01120.11210.00040.0914Chain S, catalytic domain-8.6494-18.708414.9403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'S' and resid 16 through 245)S0
2X-RAY DIFFRACTION2(chain 'S' and resid 16 through 245)S0

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