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- PDB-3osl: Structure of bovine thrombin-activatable fibrinolysis inhibitor i... -

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Basic information

Entry
Database: PDB / ID: 3osl
TitleStructure of bovine thrombin-activatable fibrinolysis inhibitor in complex with tick carboxypeptidase inhibitor
Components
  • Carboxypeptidase B2
  • Carboxypeptidase inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha/beta-hydrolase-related fold / Blood / fibrinolysis / coagulation / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Regulation of Complement cascade / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase U / acquisition of nutrients from host / metalloendopeptidase inhibitor activity / enzyme inhibitor activity / fibrinolysis / metallocarboxypeptidase activity / blood coagulation / toxin activity ...Regulation of Complement cascade / Metabolism of Angiotensinogen to Angiotensins / carboxypeptidase U / acquisition of nutrients from host / metalloendopeptidase inhibitor activity / enzyme inhibitor activity / fibrinolysis / metallocarboxypeptidase activity / blood coagulation / toxin activity / proteolysis / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
Carboxypeptidase inhibitor I68 / Carboxypeptidase inhibitor I68 / Carboxypeptidase B2 / Myotoxin/Anemone neurotoxin domain superfamily / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase
Similarity search - Domain/homology
Carboxypeptidase B2 / Carboxypeptidase inhibitor
Similarity search - Component
Biological speciesRhipicephalus bursa (arthropod)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6 Å
AuthorsValnickova, Z. / Sanglas, L. / Arolas, J.L. / Petersen, S.V. / Schar, C. / Otzen, D. / Aviles, F.X. / Gomis-Ruth, F.X. / Enghild, J.J.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Flexibility of the Thrombin-activatable Fibrinolysis Inhibitor Pro-domain Enables Productive Binding of Protein Substrates.
Authors: Valnickova, Z. / Sanglas, L. / Arolas, J.L. / Petersen, S.V. / Schar, C. / Otzen, D. / Aviles, F.X. / Gomis-Ruth, F.X. / Enghild, J.J.
#1: Journal: J.Thromb.Haemost. / Year: 2010
Title: Insights into the molecular inactivation mechanism of human activated thrombin-activatable fibrinolysis inhibitor.
Authors: Sanglas, L. / Arolas, J.L. / Valnickova, Z. / Aviles, F.X. / Enghild, J.J. / Gomis-Ruth, F.X.
#2: Journal: Mol.Cell / Year: 2008
Title: Structure of activated thrombin-activatable fibrinolysis inhibitor, a molecular link between coagulation and fibrinolysis.
Authors: Sanglas, L. / Valnickova, Z. / Arolas, J.L. / Pallares, I. / Guevara, T. / Sola, M. / Kristensen, T. / Enghild, J.J. / Aviles, F.X. / Gomis-Ruth, F.X.
History
DepositionSep 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 27, 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase B2
B: Carboxypeptidase inhibitor
C: Carboxypeptidase B2
D: Carboxypeptidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8146
Polymers108,6844
Non-polymers1312
Water00
1
A: Carboxypeptidase B2
B: Carboxypeptidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4073
Polymers54,3422
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-46 kcal/mol
Surface area15710 Å2
MethodPISA
2
C: Carboxypeptidase B2
D: Carboxypeptidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4073
Polymers54,3422
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-46 kcal/mol
Surface area15640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.100, 279.100, 279.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Carboxypeptidase B2


Mass: 46534.797 Da / Num. of mol.: 2 / Fragment: UNP residues 23-423 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: blood / References: UniProt: Q2KIG3, carboxypeptidase U
#2: Protein Carboxypeptidase inhibitor / TCI


Mass: 7806.957 Da / Num. of mol.: 2 / Fragment: UNP residues 23-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus bursa (arthropod) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5EPH2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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: 8.33 Å3/Da / Density % sol: 83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2.0 M (NH4)2SO4, 0.2 M Li2SO4, 0.1 M CAPS, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 6→50 Å / Num. all: 9806 / Num. obs: 9806 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 6→6.32 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
REFMAC5.5.0046refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6→50 Å / Cor.coef. Fo:Fc: 0.811 / Cor.coef. Fo:Fc free: 0.816 / SU B: 293.022 / SU ML: 1.31 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.609 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Due to the very low resolution of the diffraction data (6A), the protomers--which correspond to 100% identical chemical species--were properly oriented and translation according to the ...Details: Due to the very low resolution of the diffraction data (6A), the protomers--which correspond to 100% identical chemical species--were properly oriented and translation according to the Patterson search solution and thereafter just subjected to rigid-body and TLS refinement with REFMAC5. Therefore, clashes with symmetry-equivalent molecules may occur at specific points of the structure.
RfactorNum. reflection% reflectionSelection details
Rfree0.32036 739 7.6 %RANDOM
Rwork0.31255 ---
all0.31314 9806 --
obs0.31314 9014 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.71 Å2
Refinement stepCycle: LAST / Resolution: 6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 2 0 5936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226154
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.9438312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.79523.239284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.472151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7311536
X-RAY DIFFRACTIONr_chiral_restr0.1050.2848
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214664
X-RAY DIFFRACTIONr_mcbond_it0.8391.53676
X-RAY DIFFRACTIONr_mcangle_it1.4625914
X-RAY DIFFRACTIONr_scbond_it2.30332478
X-RAY DIFFRACTIONr_scangle_it3.6944.52398
LS refinement shellResolution: 6.001→6.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 53 -
Rwork0.32 637 -
obs--100 %
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)
14.8757-0.3711-0.74532.72850.57052.0164-0.0816-0.1002-0.14550.28410.02440-0.1634-0.05650.05730.0590.0128-0.00330.00530.00140.005143.802630.950672.1934
20.15180.1884-0.27162.2277-0.00240.55290.0056-0.0116-0.00160.1323-0.00830.0736-0.00410.02110.00270.01030.00090.00630.00140.00130.008522.995338.189280.1623
34.8092-0.3564-0.14871.37030.86973.54350.0525-0.0375-0.0020.0282-0.1309-0.04230.4015-0.12150.07840.0503-0.00850.01260.01380.00280.005240.61665.84643.7898
41.10940.34971.36920.97970.57042.63330.0244-0.03020.3114-0.0598-0.3259-0.24370.48780.35750.30140.27940.14640.1050.40550.03560.269461.07281.700633.4414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A118 - 423
2X-RAY DIFFRACTION1A999
3X-RAY DIFFRACTION2B1 - 74
4X-RAY DIFFRACTION3C118 - 423
5X-RAY DIFFRACTION3C999
6X-RAY DIFFRACTION4D1 - 74

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