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- PDB-1j34: Crystal Structure of Mg(II)-and Ca(II)-bound Gla Domain of Factor... -

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Basic information

Entry
Database: PDB / ID: 1j34
TitleCrystal Structure of Mg(II)-and Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein
Components
  • (coagulation factor IX-binding protein ...) x 2
  • Coagulation factor IX
KeywordsProtein binding/Blood clotting / MAGNESIUM ION / CALCIUM ION / GLA DOMAIN / Protein binding-Blood clotting COMPLEX
Function / homology
Function and homology information


coagulation factor IXa / zymogen activation / blood coagulation / toxin activity / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / magnesium ion binding / proteolysis ...coagulation factor IXa / zymogen activation / blood coagulation / toxin activity / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / magnesium ion binding / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Lectin C-type domain / C-type lectin domain profile. ...: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / Coagulation Factor Xa inhibitory site / EGF-like domain / C-type lectin fold / 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 / 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 / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha Beta
Similarity search - Domain/homology
Coagulation factor IX / Snaclec coagulation factor IX/factor X-binding protein subunit A / Snaclec coagulation factor IX/factor X-binding protein subunit B / Snaclec coagulation factor IX-binding protein subunit A
Similarity search - Component
Biological speciesTrimeresurus flavoviridis (habu)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsShikamoto, Y. / Morita, T. / Fujimoto, Z. / Mizuno, H.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of Mg2+- and Ca2+-bound Gla Domain of Factor IX Complexed with Binding Protein
Authors: Shikamoto, Y. / Morita, T. / Fujimoto, Z. / Mizuno, H.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X
Authors: Mizuno, H. / Fujimoto, Z. / Atoda, H. / Morita, T.
#2: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of coagulation factor IX-binding protein from habu snake venom at 2.6 A: implication of central loop swapping based on deletion in the linker region
Authors: Mizuno, H. / Fujimoto, Z. / Koizumi, M. / Kano, H. / Atoda, H. / Morita, T.
History
DepositionJan 20, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: coagulation factor IX-binding protein A chain
B: coagulation factor IX-binding protein B chain
C: Coagulation factor IX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,64113
Polymers35,2883
Non-polymers35310
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-130 kcal/mol
Surface area13520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.552, 37.204, 62.626
Angle α, β, γ (deg.)90.00, 103.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-663-

HOH

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Components

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Coagulation factor IX-binding protein ... , 2 types, 2 molecules AB

#1: Protein coagulation factor IX-binding protein A chain / COAGULATION FACTOR IX BINDING PROTEIN CHAIN A


Mass: 14655.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: venom / References: UniProt: P23806, UniProt: Q7LZ71*PLUS
#2: Protein coagulation factor IX-binding protein B chain


Mass: 14455.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: venom / References: UniProt: P23807

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Coagulation factor IX


Mass: 6177.313 Da / Num. of mol.: 1 / Fragment: GLA DOMAIN / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Secretion: plasma / References: UniProt: P00741, coagulation factor IXa

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Non-polymers , 3 types, 454 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 1.77 Å3/Da / Density % sol: 29.98 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8
Details: PEG 6000, Tris-HCl, calcium chloride, magnesium chloride, pH 8, MICROBATCH, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein11
230 mMTris-HCl12pH8.0
314 %PEG600012
45 mM12CaCl2
52 mM12MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.72 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. all: 39489 / Num. obs: 39489 / % possible obs: 93.6 % / Observed criterion σ(I): -0.5 / Redundancy: 9 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 10.7
Reflection shellResolution: 1.55→1.65 Å / Rmerge(I) obs: 0.209 / Num. unique all: 3302 / % possible all: 63.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IOD

1iod


Resolution: 1.55→19.63 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 311750.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3811 10 %RANDOM
Rwork0.183 ---
obs0.185 38082 90.1 %-
all-38082 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.1992 Å2 / ksol: 0.320999 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.85 Å20 Å23.39 Å2
2--2.24 Å20 Å2
3---3.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.55→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 10 444 2934
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 447 10.4 %
Rwork0.274 3840 -
obs-3302 61.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69

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