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- PDB-1bj3: CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP... -

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Basic information

Entry
Database: PDB / ID: 1bj3
TitleCRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS
Components
  • PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN A)
  • PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN B)
KeywordsCOLLAGEN BINDING PROTEIN / COAGULATION FACTOR IX-BINDING / HETERODIMER / VENOM / HABU SNAKE / C-TYPE LECTIN SUPERFAMILY
Function / homology
Function and homology information


signaling receptor activity / toxin activity / calcium ion binding / extracellular region
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 B / Snaclec coagulation factor IX-binding protein subunit A
Similarity search - Component
Biological speciesTrimeresurus flavoviridis (habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.6 Å
AuthorsMizuno, H. / Fujimoto, Z. / Koizumi, M. / Kano, H. / Atoda, H. / Morita, T.
Citation
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.
#1: Journal: 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.
#2: Journal: J.Biochem.(Tokyo) / Year: 1995
Title: Blood Coagulation Factor Ix-Binding Protein from the Venom of Trimeresurus Flavoviridis: Purification and Characterization
Authors: Atoda, H. / Ishikawa, M. / Yoshihara, E. / Sekiya, F. / Morita, T.
History
DepositionJul 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 16, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Nov 6, 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_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.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: PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN A)
B: PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1904
Polymers29,1102
Non-polymers802
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-49 kcal/mol
Surface area12210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.569, 56.794, 39.616
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN A) / IX-BP


Mass: 14655.184 Da / Num. of mol.: 1 / Fragment: C-TYPE LECTIN CRD DOMAIN / Source method: isolated from a natural source
Details: DISULPHIDE DIMER BETWEEN A CYS79 AND B CYS75, PROTEIN COMPOSED OF HOMOLOGOUS SUBUNITS TO THE CARBOHYDRATE RECOGNITION DOMAIN OF C-TYPE LECTIN
Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: VENOM / References: PIR: JC4329, UniProt: Q7LZ71*PLUS
#2: Protein PROTEIN (COAGULATION FACTOR IX-BINDING PROTEIN B) / IX-BP


Mass: 14455.071 Da / Num. of mol.: 1 / Fragment: C-TYPE LECTIN CRD DOMAIN / Source method: isolated from a natural source
Details: DISULPHIDE DIMER BETWEEN A CYS79 AND B CYS75, PROTEIN COMPOSED OF HOMOLOGOUS SUBUNITS TO THE CARBOHYDRATE RECOGNITION DOMAIN OF C-TYPE LECTIN
Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: VENOM / References: UniProt: P23807
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREFERENCE: MATURE PROTEIN LACKS INITIAL 23 RESIDUES, B CHAIN OF IX-BINDING PROTEIN IS THE SAME AS ...REFERENCE: MATURE PROTEIN LACKS INITIAL 23 RESIDUES, B CHAIN OF IX-BINDING PROTEIN IS THE SAME AS THAT OF FACTOR IX/FACTOR X-BINDING ANTICOAGULANT PROTEIN.

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.8
Details: PROTEIN WAS CRYSTALLIZED BY MIXING WITH EQUAL VOLUME OF 60% AMMONIUM SULPHATE IN 20 MM TRI-HCL BUFFER AT PH 7.8 CONTAINING AND AT ROOM TEMPERATURE
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
33 mM1dropCaCl2
460 %ammonium sulfate1reservoir
5Tris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 7253 / % possible obs: 90 % / Observed criterion σ(I): 3 / Redundancy: 4.1 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 8.6 / % possible all: 74
Reflection
*PLUS
Num. measured all: 21947

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Processing

Software
NameVersionClassification
WEISdata scaling
DENZOdata reduction
SCALEPACKdata scaling
PHASESPROGRAM PACKAGEphasing
X-PLOR2.1refinement
WEISdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 2.6→6 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.271 367 5.6 %RANDOM
Rwork0.182 ---
obs0.182 6570 88.8 %-
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 2 83 2132
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.51
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.441.5
X-RAY DIFFRACTIONx_mcangle_it2.162
X-RAY DIFFRACTIONx_scbond_it2.132
X-RAY DIFFRACTIONx_scangle_it32.5
LS refinement shellResolution: 2.6→2.75 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 53 5.9 %
Rwork0.234 842 -
obs--73.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19X.ION
X-RAY DIFFRACTION3PARAM19X.IONTOPH19X.SOL
Software
*PLUS
Name: X-PLOR / Version: 2.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / % reflection Rfree: 5.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.51
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.33 / % reflection Rfree: 5.9 % / Rfactor Rwork: 0.234

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