[English] 日本語
Yorodumi
- PDB-1bj3: CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP... -

+
Open data


ID or keywords:

Loading...

-
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


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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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.

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more