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- PDB-3d4u: Bovine thrombin-activatable fibrinolysis inhibitor (TAFIa) in com... -

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Basic information

Entry
Database: PDB / ID: 3d4u
TitleBovine thrombin-activatable fibrinolysis inhibitor (TAFIa) in complex with tick-derived carboxypeptidase inhibitor.
Components(Carboxypeptidase ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease-inhibitor complex / Carboxypeptidase / Glycoprotein / Hydrolase / Metal-binding / Metalloprotease / Protease / Secreted / Zymogen / Blood coagulation / Fibrinolysis / Metalloenzyme inhibitor / Metalloprotease inhibitor / 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, N-terminal domain / Carboxypeptidase inhibitor I68 / Carboxypeptidase inhibitor I68 / Carboxypeptidase B2 / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / ligand-binding face of the semaphorins, domain 2 / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide ...Carboxypeptidase inhibitor, N-terminal domain / Carboxypeptidase inhibitor I68 / Carboxypeptidase inhibitor I68 / Carboxypeptidase B2 / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / ligand-binding face of the semaphorins, domain 2 / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Single Sheet / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Carboxypeptidase B2 / Carboxypeptidase inhibitor
Similarity search - Component
Biological speciesRhipicephalus bursa (arthropod)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSanglas, L. / Valnickova, Z. / Arolas, J.L. / Pallares, I. / Guevara, T. / Sola, M. / Kristensen, T. / Enghild, J.J. / Aviles, F.X. / Gomis-Ruth, F.X.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Human procarboxypeptidase B: three-dimensional structure and implications for thrombin-activatable fibrinolysis inhibitor (TAFI)
Authors: Barbosa Pereira, P.J. / Oliva, B. / Ferrer-Orta, C. / Coll, M. / Vendrell, J.
History
DepositionMay 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 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.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
Revision 1.3Oct 30, 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: Carboxypeptidase B2
B: Carboxypeptidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,50110
Polymers43,8372
Non-polymers6648
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-112 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.200, 84.200, 127.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Carboxypeptidase ... , 2 types, 2 molecules AB

#1: Protein Carboxypeptidase B2 / TAFIa


Mass: 36029.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: blood / References: UniProt: Q2KIG3, carboxypeptidase U
#2: Protein Carboxypeptidase inhibitor / Tick carboxypeptidase inhibitor / TCI


Mass: 7806.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus bursa (arthropod) / Plasmid: pBAT-4-OmpA-TCI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/DE3 / References: UniProt: Q5EPH2

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Non-polymers , 4 types, 366 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M (NH4)2SO4, 0.1M NaAcO, 10% PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 18, 2007
Details: horizontally diffracting Si (111) monochromator and Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry as the focusing system.
RadiationMonochromator: Horizontally diffracting Si (111) monochromator and Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry as the focusing system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→48.1 Å / Num. all: 62124 / Num. obs: 57962 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 20.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 9.2 / Num. unique all: 8032 / Rsym value: 0.611 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZLI

1zli


Resolution: 1.7→48.08 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.053 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.074 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17071 695 1.2 %RANDOM
Rwork0.15588 ---
all0.15606 62124 --
obs0.15606 57265 99.34 %-
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: 20.858 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 34 358 3360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223103
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9524192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.79623.239142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47315534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7321518
X-RAY DIFFRACTIONr_chiral_restr0.1070.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022340
X-RAY DIFFRACTIONr_nbd_refined0.2060.21476
X-RAY DIFFRACTIONr_nbtor_refined0.310.22083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2282
X-RAY DIFFRACTIONr_metal_ion_refined0.010.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.215
X-RAY DIFFRACTIONr_mcbond_it0.961.51906
X-RAY DIFFRACTIONr_mcangle_it1.46222961
X-RAY DIFFRACTIONr_scbond_it2.30231424
X-RAY DIFFRACTIONr_scangle_it3.6634.51231
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 55 -
Rwork0.223 3795 -
obs--90.93 %
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)
10.93470.09530.01260.68230.04550.8980.0145-0.1059-0.02210.13-0.0453-0.0370.04320.0280.0308-0.0677-0.0025-0.0035-0.0862-0.0026-0.077815.004222.880182.6778
23.6941.41130.08912.50631.01611.12210.0957-0.35120.17060.2874-0.09470.241-0.0322-0.0625-0.001-0.04020.03010.0461-0.026-0.0455-0.0711-2.334534.437993.4675
30.96910.0249-0.13381.01920.02471.06520.0162-0.11030.02520.1248-0.05410.01040.0077-0.00890.0379-0.0406-0.00150.0024-0.0391-0.0062-0.04269.017425.37883.7947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 54
2X-RAY DIFFRACTION1A59 - 92
3X-RAY DIFFRACTION1A98 - 308
4X-RAY DIFFRACTION2B1 - 74
5X-RAY DIFFRACTION3A601 - 607
6X-RAY DIFFRACTION3A2357 - 2635
7X-RAY DIFFRACTION3B514 - 859

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