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- PDB-1x2w: Crystal Structure of Apo-Habu IX-bp at pH 4.6 -

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Basic information

Entry
Database: PDB / ID: 1x2w
TitleCrystal Structure of Apo-Habu IX-bp at pH 4.6
Components(Coagulation factor ...Coagulation) x 2
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 fold ...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
RUBIDIUM ION / 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: 2.29 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 / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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 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)29,4136
Polymers29,1102
Non-polymers3024
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-55 kcal/mol
Surface area12180 Å2
MethodPISA
2
A: Coagulation factor IX/X-binding protein A chain
B: Coagulation factor IX/factor X-binding protein B chain
hetero molecules

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)58,82512
Polymers58,2214
Non-polymers6058
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10490 Å2
ΔGint-131 kcal/mol
Surface area22440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.121, 37.831, 55.828
Angle α, β, γ (deg.)90.00, 110.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-402-

RB

21A-562-

HOH

31B-270-

HOH

41B-271-

HOH

51B-280-

HOH

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Components

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Coagulation factor ... , 2 types, 2 molecules AB

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


Mass: 14655.184 Da / Num. of mol.: 1 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: Venom / References: UniProt: P23807

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Non-polymers , 4 types, 327 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-RB / RUBIDIUM ION / Rubidium


Mass: 85.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rb
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.3 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: AMMONIUM SULPHATE, RUBIDIUM ACETATE, PEGMME 2000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, 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 VII / Detector: IMAGE PLATE / Date: Sep 11, 2003 / 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: 2.29→36.2 Å / Num. all: 12105 / Num. obs: 11631 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.3
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1193 / % possible all: 89.8

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Processing

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

1bj3


Resolution: 2.29→34.68 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 984047.99 / 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
Rfree0.28 566 4.9 %RANDOM
Rwork0.214 ---
all-12064 --
obs-11542 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.2253 Å2 / ksol: 0.35875 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.77 Å20 Å24.99 Å2
2---1.12 Å20 Å2
3----4.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.29→34.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 8 323 2378
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.892.5
LS refinement shellResolution: 2.29→2.43 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.484 87 4.6 %
Rwork0.331 1801 -
obs-1889 94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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