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- PDB-1x2t: Crystal Structure of Habu IX-bp at pH 6.5 -

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Basic information

Entry
Database: PDB / ID: 1x2t
TitleCrystal Structure of Habu IX-bp at pH 6.5
Components
  • Coagulation factor IX/X-binding protein A chain
  • Coagulation factor IX/factor X-binding protein B chain
KeywordsPROTEIN BINDING / HETERODIMER / DOMAIN SWAPPING / C-TYPE LECTIN-LIKE PROTEIN
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 / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsSuzuki, N. / Fujimoto, Z. / Morita, T. / Fukamizu, A. / Mizuno, H.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: pH-Dependent Structural Changes at Ca(2+)-binding sites of Coagulation Factor IX-binding Protein
Authors: Suzuki, N. / Fujimoto, Z. / Morita, T. / Fukamizu, A. / Mizuno, H.
History
DepositionApr 26, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 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
A: Coagulation factor IX/X-binding protein A chain
B: Coagulation factor IX/factor X-binding protein B chain
C: Coagulation factor IX/X-binding protein A chain
D: Coagulation factor IX/factor X-binding protein B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,85710
Polymers58,2214
Non-polymers6376
Water10,233568
1
A: Coagulation factor IX/X-binding protein A chain
B: Coagulation factor IX/factor X-binding protein B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4295
Polymers29,1102
Non-polymers3183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-49 kcal/mol
Surface area11980 Å2
MethodPISA
2
C: Coagulation factor IX/X-binding protein A chain
D: Coagulation factor IX/factor X-binding protein B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4295
Polymers29,1102
Non-polymers3183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-50 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.710, 63.509, 66.902
Angle α, β, γ (deg.)90.00, 117.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Coagulation factor IX/X-binding protein A chain


Mass: 14655.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: Venom / References: UniProt: Q7LZ71
#2: Protein Coagulation factor IX/factor X-binding protein B chain / IX/X-BP


Mass: 14455.071 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: PEG 1000, PEG 8000, calcium chloride, MES, pH 6.5, MICROBATCH, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 17, 2001 / Details: Mirrors
RadiationMonochromator: COLLIMATION / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→54.1 Å / Num. all: 48268 / Num. obs: 47809 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.8
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4797 / % possible all: 92.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJ3

1bj3


Resolution: 1.72→33.26 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1224138.88 / 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
Rfree0.222 2383 5 %RANDOM
Rwork0.191 ---
all-48267 --
obs-47807 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.0938 Å2 / ksol: 0.347911 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.26 Å2
2--3.74 Å20 Å2
3----3.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.72→33.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 30 568 4698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 1.72→1.83 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 393 5.1 %
Rwork0.308 7269 -
obs-7269 95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2pg4.parampg4.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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