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- PDB-4bxw: Crystal Structure of the Prothrombinase Complex from the Venom of... -

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Basic information

Entry
Database: PDB / ID: 4bxw
TitleCrystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis
Components
  • COAGULATION FACTOR V
  • FACTOR XA
KeywordsBLOOD CLOTTING / BLOOD COAGULATION / PROTHROMBINASE / FACTOR V / FACTOR X / HYDROLASE / PROTEASE
Function / homology
Function and homology information


induction of blood coagulation in another organism / envenomation resulting in positive regulation of blood coagulation in another organism / peptidase activator activity / coagulation factor Xa / blood coagulation / toxin activity / copper ion binding / serine-type endopeptidase activity / calcium ion binding / protein-containing complex ...induction of blood coagulation in another organism / envenomation resulting in positive regulation of blood coagulation in another organism / peptidase activator activity / coagulation factor Xa / blood coagulation / toxin activity / copper ion binding / serine-type endopeptidase activity / calcium ion binding / protein-containing complex / proteolysis / extracellular region
Similarity search - Function
Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / F5/8 type C domain ...Coagulation factor 5/8-like / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Laminin / Coagulation Factor Xa inhibitory site / Laminin / Multicopper oxidase, N-terminal / Multicopper oxidase / EGF-like domain / 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. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Cupredoxin / Galactose-binding-like domain superfamily / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GLU-GLY-ARG-CHLOROMETHYL KETONE / Chem-0GJ / Venom prothrombin activator pseutarin-C catalytic subunit / Coagulation factor V / Venom prothrombin activator pseutarin-C catalytic subunit
Similarity search - Component
Biological speciesPSEUDONAJA TEXTILIS (eastern brown snake)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsLechtenberg, B.C. / Murray-Rust, T.A. / Johnson, D.J.D. / Adams, T.E. / Krishnaswamy, S. / Camire, R.M. / Huntington, J.A.
CitationJournal: Blood / Year: 2013
Title: Crystal Structure of the Prothrombinase Complex from the Venom of Pseudonaja Textilis.
Authors: Lechtenberg, B.C. / Murray-Rust, T.A. / Johnson, D.J. / Adams, T.E. / Krishnaswamy, S. / Camire, R.M. / Huntington, J.A.
History
DepositionJul 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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: FACTOR XA
B: FACTOR XA
F: COAGULATION FACTOR V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2319
Polymers96,1403
Non-polymers1,0916
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-22.6 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.310, 179.310, 179.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-230-

ARG

21B-230-

ARG

31B-2061-

HOH

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABF

#1: Protein FACTOR XA


Mass: 47041.273 Da / Num. of mol.: 2 / Fragment: EGF2-CATALYTIC DOMAIN CONSTRUCT, RESIDUES 41-463
Source method: isolated from a genetically manipulated source
Details: PSEUTARIN C CATALYTIC SUBUNIT
Source: (gene. exp.) PSEUDONAJA TEXTILIS (eastern brown snake)
Organ: VENOM GLAND / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q6IT10, UniProt: Q56VR3*PLUS
#2: Protein/peptide COAGULATION FACTOR V / FACTOR V A2 PEPTIDE


Mass: 2057.041 Da / Num. of mol.: 1 / Fragment: A2 PEPTIDE, RESIDUES 693-710 / Source method: obtained synthetically / Details: 663 TO 680 OF P. TEXTILIS FV / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: Q593B6

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Non-polymers , 4 types, 167 molecules

#3: Chemical ChemComp-0GJ / L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 395.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28ClN6O5 / References: GLU-GLY-ARG-CHLOROMETHYL KETONE
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsEGF2-CATALYTIC DOMAINS ONLY

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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: 3.83 Å3/Da / Density % sol: 67.89 % / Description: NONE
Crystal growpH: 5.5 / Details: 45MM MES PH 5.5 AND 5.6% PVP K12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.527
11-H, L, K20.473
ReflectionResolution: 2.71→73.2 Å / Num. obs: 26001 / % possible obs: 1 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3
Reflection shellResolution: 2.71→2.85 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL BASED ON PDB ENTRY 1HCG

1hcg


Resolution: 2.71→73.2 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.823 / SU B: 11.594 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AUTO LOCAL NCS USED IN REFMAC
RfactorNum. reflection% reflectionSelection details
Rfree0.23308 1351 5.2 %RANDOM
Rwork0.15537 ---
obs0.15917 24649 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.196 Å2
Baniso -1Baniso -2Baniso -3
1--24.82 Å27.74 Å2-22.16 Å2
2---29.23 Å2-15.2 Å2
3---54.04 Å2
Refinement stepCycle: LAST / Resolution: 2.71→73.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 69 161 4530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0194483
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6691.9566097
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1035578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90324.235170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39615663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3751515
X-RAY DIFFRACTIONr_chiral_restr0.0470.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0213365
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.714→2.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 108 -
Rwork0.325 1763 -
obs--98.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.1788-1.9898-0.60494.27691.01833.78080.1195-0.2861-0.2630.49090.2219-0.3856-0.02850.4929-0.34130.20830.0895-0.04340.1714-0.02560.0827-12.227616.978416.5053
21.956-0.24360.36412.11870.01590.8486-0.0264-0.0785-0.02160.10940.01360.20060.031-0.30340.01290.12370.05160.05190.18620.0390.1251-29.101513.8824-3.1769
32.0791-0.0799-0.40071.2679-0.49130.8181-0.04540.0578-0.0601-0.05640.02930.1879-0.0014-0.26780.01610.1140.0699-0.00520.17790.01140.0887-30.052319.8335-10.6533
40.7267-0.355-0.00751.51450.02280.76030.01590.0554-0.0561-0.0077-0.02030.03330.0198-0.05820.00440.09210.02870.02030.11420.02320.0819-19.0837.9445-5.563
50.48550.5450.74380.74391.86079.17540.1349-0.06150.04210.00230.03210.0261-0.67270.358-0.1670.1622-0.0327-0.00450.2487-0.04050.3388-13.00923.5215-3.1697
62.7686-3.048-1.90674.12171.03272.8549-0.17980.202-0.450.42290.02350.6579-0.3341-0.50910.15630.23690.0722-0.09260.1697-0.01760.4386-32.875261.6258-22.1264
70.8691-0.6908-0.66853.48763.26373.07410.1560.12990.1815-0.373-0.0015-0.2433-0.3858-0.0079-0.15450.2656-0.0764-0.04710.12120.08460.2959-19.105355.9958-30.1951
81.3956-0.1092-0.38971.7115-0.08541.4523-0.13810.1215-0.0182-0.03470.1173-0.1880.03740.2440.02080.10020.0151-0.0320.12850.02880.138-15.920735.87-26.2558
91.2425-0.01090.34050.85630.10351.3365-0.1150.18940.1344-0.05480.0531-0.0366-0.12890.04020.06190.1031-0.0178-0.05110.10190.05690.1532-25.123444.3684-35.5333
101.1970.2174-0.19551.9045-0.0651.7096-0.14950.15190.0767-0.09940.04530.14-0.0243-0.00390.10420.0837-0.0019-0.04220.13390.04680.1802-28.071440.5177-33.2578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A89 - 131
2X-RAY DIFFRACTION2A132 - 214
3X-RAY DIFFRACTION3A215 - 252
4X-RAY DIFFRACTION4A253 - 398
5X-RAY DIFFRACTION5A399 - 410
6X-RAY DIFFRACTION6B89 - 121
7X-RAY DIFFRACTION7B122 - 174
8X-RAY DIFFRACTION8B175 - 276
9X-RAY DIFFRACTION9B277 - 336
10X-RAY DIFFRACTION10B337 - 411

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