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- PDB-1ixx: CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX... -

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Entry
Database: PDB / ID: 1ixx
TitleCRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS
Components(COAGULATION FACTORS IX/X-BINDING PROTEIN) x 2
KeywordsCOAGULATION FACTOR BINDING / C-TYPE LECTIN / GLA-DOMAIN BINDING / C-TYPE CRD MOTIF / LOOP EXCHANGED DIMER
Function / homology
Function and homology information


toxin activity / calcium ion binding / 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 / 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 ...: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / 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 / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Snaclec coagulation factor IX/factor X-binding protein subunit A / Snaclec coagulation factor IX/factor X-binding protein subunit B
Similarity search - Component
Biological speciesTrimeresurus flavoviridis (habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5 Å
AuthorsMizuno, H. / Fujimoto, Z. / Koizumi, M. / Kano, H.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Structure of coagulation factors IX/X-binding protein, a heterodimer of C-type lectin domains.
Authors: Mizuno, H. / Fujimoto, Z. / Koizumi, M. / Kano, H. / Atoda, H. / Morita, T.
History
DepositionMay 1, 1997Processing site: BNL
Revision 1.0May 6, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COAGULATION FACTORS IX/X-BINDING PROTEIN
B: COAGULATION FACTORS IX/X-BINDING PROTEIN
C: COAGULATION FACTORS IX/X-BINDING PROTEIN
D: COAGULATION FACTORS IX/X-BINDING PROTEIN
E: COAGULATION FACTORS IX/X-BINDING PROTEIN
F: COAGULATION FACTORS IX/X-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,14212
Polymers87,9026
Non-polymers2406
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: COAGULATION FACTORS IX/X-BINDING PROTEIN
D: COAGULATION FACTORS IX/X-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3814
Polymers29,3012
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-48 kcal/mol
Surface area11910 Å2
MethodPISA
3
A: COAGULATION FACTORS IX/X-BINDING PROTEIN
B: COAGULATION FACTORS IX/X-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3814
Polymers29,3012
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-49 kcal/mol
Surface area11920 Å2
MethodPISA
4
E: COAGULATION FACTORS IX/X-BINDING PROTEIN
F: COAGULATION FACTORS IX/X-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3814
Polymers29,3012
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-50 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.200, 85.700, 65.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.493228, -0.834005, 0.24731), (0.795078, -0.316751, -0.517161), (0.352954, -0.451709, 0.819379)47.67068, 13.68843, 3.53878
2given(-0.534691, 0.765416, 0.358111), (-0.822233, -0.373424, -0.42952), (-0.195034, -0.524111, 0.829017)12.95387, 46.20907, 15.27883
DetailsTHE ASYMMETRIC UNIT CONTAINS THREE DIMERS ARRANGED AROUND A PSEUDO TRIAD.

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Components

#1: Protein COAGULATION FACTORS IX/X-BINDING PROTEIN / IX/X-BP


Mass: 14845.512 Da / Num. of mol.: 3 / Fragment: C-TYPE LECTIN DOMAIN / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: VENOM / References: UniProt: P23806
#2: Protein COAGULATION FACTORS IX/X-BINDING PROTEIN / IX/X-BP


Mass: 14455.071 Da / Num. of mol.: 3 / Fragment: C-TYPE LECTIN DOMAIN / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: VENOM / References: UniProt: P23807
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIX/X-BP IS A DISULFIDE-LINKED HETERODIMER PROTEIN CONSISTING OF HOMOLOGOUS SUBUNITS. EACH SUBUNIT ...IX/X-BP IS A DISULFIDE-LINKED HETERODIMER PROTEIN CONSISTING OF HOMOLOGOUS SUBUNITS. EACH SUBUNIT IS HOMOLOGOUS TO THE CARBOHYDRATE-RECOGNITION DOMAIN OF C-TYPE LECTIN, AND IX/X-BP BELONGS TO THE C-TYPE LECTIN SUPERFAMILY.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growpH: 7.8
Details: 60% SATURATED AMMONIUM SULFATE, 20 MM TRIS-HCL, 3 MM CACL2, PH 7.8
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Mizuno, H., (1991) J. Mol. Biol., 220, 225.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1reservoir
23 mM1reservoirCaCl2
360 %satammonium sulfate1reservoir
410 mg/mlprotein1drop
520 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 28, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 29883 / % possible obs: 87 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 39
Reflection shellResolution: 2.5→2.61 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 6 / % possible all: 75

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.5→6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: PARAMETER AND TOPOLOGY FILES FOR SOLVENT WERE PREPARED FROM TUTORIAL FILES IN THE X-PLOR MANUAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1228 5 %RANDOM
Rwork0.178 ---
obs0.178 25211 80 %-
Displacement parametersBiso mean: 29.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-6 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6177 0 6 146 6329
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.291.5
X-RAY DIFFRACTIONx_mcangle_it6.32
X-RAY DIFFRACTIONx_scbond_it6.412
X-RAY DIFFRACTIONx_scangle_it8.692.5
LS refinement shellResolution: 2.5→2.64 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 166 5 %
Rwork0.265 3301 -
obs--66.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19
LS refinement shell
*PLUS
Rfactor Rfree: 0.3

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