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- PDB-5jb9: Crystal structure of factor IXa K98T variant in complex with PPACK -

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Basic information

Entry
Database: PDB / ID: 5jb9
TitleCrystal structure of factor IXa K98T variant in complex with PPACK
Components(Coagulation factor ...) x 2
KeywordsHYDROLASE / BLOOD CLOTTING / GLYCOPROTEIN / HAEMOSTASIS
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 / Laminin / Coagulation Factor Xa inhibitory site / Laminin / 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. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Laminin / Coagulation Factor Xa inhibitory site / Laminin / 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 / Ribbon / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Coagulation factor IX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 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 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jan 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

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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)33,1305
Polymers32,5582
Non-polymers5723
Water5,368298
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-20 kcal/mol
Surface area13540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.270, 67.050, 97.150
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, 301 molecules

#3: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / References: D-Phe-Pro-Arg-CH2Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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.: 298 / 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: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 6 mg/mL protein/inhibitor complex 0.1 M MES pH 6.5 18% 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: 1.3→14.92 Å / Num. obs: 71402 / % possible obs: 99.43 % / Redundancy: 4.5 % / Biso Wilson estimate: 15.58 Å2 / Rmerge(I) obs: 0.06481 / Net I/σ(I): 9.51
Reflection shellResolution: 1.3→1.346 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.6968 / Mean I/σ(I) obs: 1.81 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
iMOSFLM7.11data 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: 2wph

2wph


Resolution: 1.3→14.919 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.85
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 3546 4.97 %HKL reflections copied from pdb entry 2wph
Rwork0.1509 ---
obs0.1522 71374 99.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.83 Å2 / Biso mean: 31.1078 Å2 / Biso min: 10.41 Å2
Refinement stepCycle: final / Resolution: 1.3→14.919 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 68 312 2605
Biso mean--19.38 36.92 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172400
X-RAY DIFFRACTIONf_angle_d1.5183237
X-RAY DIFFRACTIONf_chiral_restr0.08352
X-RAY DIFFRACTIONf_plane_restr0.009422
X-RAY DIFFRACTIONf_dihedral_angle_d13.963859
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.31780.28161600.2826622822100
1.3178-1.33660.30161500.248626902840100
1.3366-1.35660.24541410.24726912832100
1.3566-1.37770.2911190.235326972816100
1.3777-1.40030.23551260.224226982824100
1.4003-1.42440.21891290.211427382867100
1.4244-1.45030.19821270.203426792806100
1.4503-1.47820.20611330.194727292862100
1.4782-1.50830.21311320.1942650278299
1.5083-1.54110.19071250.18532722284799
1.5411-1.57690.21411470.17227072854100
1.5769-1.61630.17311520.16326892841100
1.6163-1.660.18481380.15462685282399
1.66-1.70870.18561390.1512618275796
1.7087-1.76380.16561480.14792566271495
1.7638-1.82670.18261430.148627132856100
1.8267-1.89970.20941520.150727042856100
1.8997-1.9860.1511320.144727382870100
1.986-2.09040.15091600.134527272887100
2.0904-2.2210.15581390.136727542893100
2.221-2.39190.16851490.142127222871100
2.3919-2.63140.16371620.139627582920100
2.6314-3.00940.16771470.146727772924100
3.0094-3.78130.17241550.13552763291899
3.7813-14.91970.16311410.137229513092100
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)
11.95630.5772-1.07092.2803-0.10711.0914-0.57840.7923-0.1704-0.90370.4890.0804-0.04510.33220.03640.489-0.1711-0.00860.43180.00380.1805Chain E, EGF2 domain6.5317-20.927-40.1048
22.49460.2804-0.04851.3793-0.03931.1194-0.12090.1068-0.04410.00590.0596-0.00020.10750.01190.04860.10620.0049-0.00280.09270.00090.0752Chain S, catalytic domain8.5881-18.6595-14.7283
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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