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- PDB-5jbc: Crystal structure of factor IXa variant V16I K98T Y177T I213V in ... -

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Basic information

Entry
Database: PDB / ID: 5jbc
TitleCrystal structure of factor IXa variant V16I K98T Y177T I213V in complex with PPACK
Components(Coagulation factor IX) x 2
KeywordsHYDROLASE / Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone
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
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: 1.9 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 1.1Dec 21, 2016Group: Non-polymer description
Revision 1.2Jan 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 1.3Oct 23, 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)32,9904
Polymers32,4962
Non-polymers4942
Water2,972165
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-23 kcal/mol
Surface area13700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.340, 65.800, 97.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: 26100.672 Da / Num. of mol.: 1 / Mutation: V16I K98T Y177T I213V
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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
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: 2.18 Å3/Da / Density % sol: 43.69 %
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, 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: Sep 29, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.9→27.25 Å / Num. obs: 23122 / % possible obs: 100 % / Redundancy: 16.3 % / Biso Wilson estimate: 25.07 Å2 / Rmerge(I) obs: 0.1505 / Net I/σ(I): 12.35
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.8739 / Mean I/σ(I) obs: 3.14 / % 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
REFMAC5.8.0078refinement
Coot0.8.1-premodel building
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wph

2wph


Resolution: 1.9→27.25 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1174 5.08 %HKL reflections copied from pdb entry 2wph
Rwork0.1659 21945 --
obs0.1683 23119 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 224.86 Å2 / Biso mean: 45.21 Å2 / Biso min: 12.34 Å2
Refinement stepCycle: final / Resolution: 1.9→27.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 64 166 2450
Biso mean--28.56 35.91 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052325
X-RAY DIFFRACTIONf_angle_d0.9013131
X-RAY DIFFRACTIONf_chiral_restr0.036347
X-RAY DIFFRACTIONf_plane_restr0.004403
X-RAY DIFFRACTIONf_dihedral_angle_d13.072831
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9001-1.98660.30131310.243827132844
1.9866-2.09130.27941610.21226822843
2.0913-2.22230.21271350.18527122847
2.2223-2.39380.21941490.173226932842
2.3938-2.63450.22891620.17227232885
2.6345-3.01530.21121420.182127352877
3.0153-3.79730.21941550.156327702925
3.7973-27.25770.17071390.136629173056
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)
11.2811-0.3795-0.11442.7567-0.27082.2014-0.7096-1.037-0.40141.14540.5235-0.12340.2772-0.2194-0.03920.68860.2243-0.01140.57710.03140.2678Chain E, EGF2 domain-6.6512-20.383640.1587
22.5458-0.2837-0.20062.08180.4091.7152-0.0812-0.1208-0.00290.02730.0370.00120.0942-0.02850.04310.1325-0.0013-0.0070.13110.00390.1201Chain S, catalytic domain-8.9398-18.112214.8851
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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