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- PDB-1iod: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X... -

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Basic information

Entry
Database: PDB / ID: 1iod
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X
Components
  • (COAGULATION FACTOR X BINDING PROTEIN) x 2
  • COAGULATION FACTOR X GLA DOMAIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / calcium bridging / domain swapping / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


coagulation factor Xa / blood coagulation / toxin activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / 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 / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Lectin C-type domain / C-type lectin domain profile. ...: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / 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 / Coagulation Factor Xa inhibitory site / EGF-like domain / C-type lectin fold / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Alpha Beta
Similarity search - Domain/homology
Coagulation factor X / Snaclec anticoagulant protein subunit B / Snaclec agkisacutacin subunit A
Similarity search - Component
Biological speciesDeinagkistrodon acutus (Chinese moccasin)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMizuno, H. / Fujimoto, Z. / Atoda, H. / Morita, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2001
Title: Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X.
Authors: Mizuno, H. / Fujimoto, Z. / Atoda, H. / Morita, T.
History
DepositionFeb 27, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAGULATION FACTOR X BINDING PROTEIN
B: COAGULATION FACTOR X BINDING PROTEIN
G: COAGULATION FACTOR X GLA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,47815
Polymers34,9973
Non-polymers48112
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-134 kcal/mol
Surface area13630 Å2
MethodPISA
2
A: COAGULATION FACTOR X BINDING PROTEIN
B: COAGULATION FACTOR X BINDING PROTEIN
G: COAGULATION FACTOR X GLA DOMAIN
hetero molecules

A: COAGULATION FACTOR X BINDING PROTEIN
B: COAGULATION FACTOR X BINDING PROTEIN
G: COAGULATION FACTOR X GLA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,95630
Polymers69,9946
Non-polymers96224
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area12920 Å2
ΔGint-283 kcal/mol
Surface area26710 Å2
MethodPISA
3
A: COAGULATION FACTOR X BINDING PROTEIN
B: COAGULATION FACTOR X BINDING PROTEIN
G: COAGULATION FACTOR X GLA DOMAIN
hetero molecules

A: COAGULATION FACTOR X BINDING PROTEIN
B: COAGULATION FACTOR X BINDING PROTEIN
G: COAGULATION FACTOR X GLA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,95630
Polymers69,9946
Non-polymers96224
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12740 Å2
ΔGint-283 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.76, 99.76, 90.42
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-511-

CA

21A-512-

CA

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Components

#1: Protein COAGULATION FACTOR X BINDING PROTEIN


Mass: 14682.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / References: UniProt: Q9IAM1*PLUS
#2: Protein COAGULATION FACTOR X BINDING PROTEIN


Mass: 14580.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / References: UniProt: Q9DEF8*PLUS
#3: Protein/peptide COAGULATION FACTOR X GLA DOMAIN


Mass: 5734.670 Da / Num. of mol.: 1 / Fragment: GLA DOMAIN(RESIDUES 41-84) / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00743, coagulation factor Xa
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: PEG8000, calcium chloride, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1reservoir
212 %PEG80001reservoir
35 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: May 11, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 109232 / Num. obs: 20411 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.3
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.33 / Num. unique all: 3048 / % possible all: 90.3
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 109232
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 92.5 % / Num. unique obs: 3206 / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY

Resolution: 2.3→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 1857 RANDOM
Rwork0.201 --
all0.225 18805 -
obs0.201 18805 -
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-6 Å
Luzzati sigma a0.36 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 12 181 2653
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.301 296 -
Rwork0.302 --
obs-2618 87.7 %
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.3 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.5
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.302

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