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- PDB-3d66: Crystal structure of Thrombin-Activatable Fibrinolysis Inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 3d66
TitleCrystal structure of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI)
ComponentsCarboxypeptidase B2
KeywordsHYDROLASE / alpha/beta hydrolase fold / Carboxypeptidase / Glycoprotein / Metal-binding / Metalloprotease / Protease / Secreted / Zymogen
Function / homology
Function and homology information


carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / metallocarboxypeptidase activity / negative regulation of fibrinolysis / Metabolism of Angiotensinogen to Angiotensins / fibrinolysis / Regulation of Complement cascade / liver regeneration ...carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / metallocarboxypeptidase activity / negative regulation of fibrinolysis / Metabolism of Angiotensinogen to Angiotensins / fibrinolysis / Regulation of Complement cascade / liver regeneration / cellular response to glucose stimulus / protein catabolic process / blood coagulation / response to xenobiotic stimulus / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region
Similarity search - Function
Carboxypeptidase B2 / Metallocarboxypeptidase-like / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases ...Carboxypeptidase B2 / Metallocarboxypeptidase-like / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBrondijk, T.H.C. / Huizinga, E.G.
CitationJournal: Blood / Year: 2008
Title: Crystal structures of TAFI elucidate the inactivation mechanism of activated TAFI: a novel mechanism for enzyme autoregulation
Authors: Marx, P.F. / Brondijk, T.H. / Plug, T. / Romijn, R.A. / Hemrika, W. / Meijers, J.C.M. / Huizinga, E.G.
History
DepositionMay 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)148,19315
Polymers146,0063
Non-polymers2,18712
Water00
1
A: Carboxypeptidase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6196
Polymers48,6691
Non-polymers9505
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carboxypeptidase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6196
Polymers48,6691
Non-polymers9505
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Carboxypeptidase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9553
Polymers48,6691
Non-polymers2872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.740, 161.740, 139.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A B C
21
31

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAA1 - 36424 - 387
21ALAALALEULEUBB1 - 36424 - 387
31ALAALALEULEUCC1 - 36424 - 387
12TYRTYRNAGNAGAA - G370 - 604393
22TYRTYRNAGNAGBB - L370 - 604393
32TYRTYRNAGNAGCC - N370 - 604393

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Components

#1: Protein Carboxypeptidase B2 / Carboxypeptidase U / CPU / Thrombin-activable fibrinolysis inhibitor / TAFI / Plasma carboxypeptidase B / pCPB


Mass: 48668.684 Da / Num. of mol.: 3 / Fragment: UNP residues 24-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPB2 / Plasmid: pABC345 / Cell (production host): Embryonic Kidney cell / Cell line (production host): HEK293ES / Production host: HOMO SAPIENS (human) / References: UniProt: Q96IY4, carboxypeptidase U
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY
Sequence detailsTHE SEQUENCE IS A NATURALLY OCCURING VARIANT BASED ON DBSNP:RS3742264 (NCBI).

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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: 3.61 Å3/Da / Density % sol: 65.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 16-18% PEG 3000, 0.18-0.22mM Na/K-tartrate, 50mM L-glutamate, 50 mM L-arginine, pH 6.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.26206 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26206 Å / Relative weight: 1
ReflectionResolution: 3.1→49.51 Å / Num. all: 38621 / Num. obs: 38593 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 8.6 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 13.9
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata scaling
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KWM

1kwm


Resolution: 3.1→49.51 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.913 / SU B: 39.948 / SU ML: 0.31 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24038 1953 5.1 %RANDOM
Rwork0.20442 ---
obs0.20621 36638 99.99 %-
all-36638 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.939 Å2
Baniso -1Baniso -2Baniso -3
1-3.98 Å21.99 Å20 Å2
2--3.98 Å20 Å2
3----5.98 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9735 0 129 0 9864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02210152
X-RAY DIFFRACTIONr_bond_other_d0.0030.026800
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.94113797
X-RAY DIFFRACTIONr_angle_other_deg1.0993.00216430
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.44951200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06323.522477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.734151650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1741557
X-RAY DIFFRACTIONr_chiral_restr0.0980.21509
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211148
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022157
X-RAY DIFFRACTIONr_nbd_refined0.2460.22423
X-RAY DIFFRACTIONr_nbd_other0.210.27081
X-RAY DIFFRACTIONr_nbtor_refined0.2040.24989
X-RAY DIFFRACTIONr_nbtor_other0.0940.25454
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2184
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1020.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3420.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9591.57594
X-RAY DIFFRACTIONr_mcbond_other0.1261.52421
X-RAY DIFFRACTIONr_mcangle_it1.19829723
X-RAY DIFFRACTIONr_scbond_it1.5834975
X-RAY DIFFRACTIONr_scangle_it2.3694.54074
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5447 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.050.05
2Btight positional0.060.05
3Ctight positional0.050.05
1Atight thermal4.56
2Btight thermal4.82
3Ctight thermal2.16
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 130 -
Rwork0.312 2677 -
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)
15.32970.89323.03824.26871.01396.40760.2767-0.4780.3651-0.1225-0.2657-0.4135-0.7662-0.0873-0.0110.07960.0188-0.1359-0.36980.0884-0.070444.841356.06950.3523
21.5706-0.56171.0983.31312.23436.35450.1451-0.16020.0357-0.0674-0.3492-0.2198-0.0674-0.45550.2041-0.39540.068-0.1227-0.37380.1171-0.313133.329436.714937.7149
35.80161.5369-4.11393.217-1.44856.3939-0.19310.2285-0.4768-0.2007-0.0234-0.65990.8360.52660.21650.1180.51720.1846-0.11240.25720.17568.7218-15.292112.9578
41.9171-0.1123-2.03034.2341-0.77545.2650.0655-0.06480.26370.2776-0.1511-0.6064-0.04560.1130.0856-0.16990.10340.0409-0.33670.1855-0.221447.995-5.333324.7435
53.47241.6934-1.52245.7151-2.73346.2778-0.28840.15760.3561-0.0765-0.0017-0.6911-0.24470.83910.2901-0.22780.08210.00120.48990.34980.40264.416237.0447-15.1021
62.8564-0.6926-1.8461.895-1.6855.6815-0.21780.11020.3085-0.093-0.0292-0.3959-0.07130.04730.247-0.39570.1633-0.0249-0.2950.2183-0.164442.498629.2643-5.1166
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 9224 - 115
2X-RAY DIFFRACTION1AD - G601 - 6041
3X-RAY DIFFRACTION2AA93 - 401116 - 424
4X-RAY DIFFRACTION2AM5011
5X-RAY DIFFRACTION3BB1 - 9224 - 115
6X-RAY DIFFRACTION3BH - K601 - 6041
7X-RAY DIFFRACTION4BB93 - 401116 - 424
8X-RAY DIFFRACTION4BN5011
9X-RAY DIFFRACTION5CC1 - 9224 - 115
10X-RAY DIFFRACTION5CL6041
11X-RAY DIFFRACTION6CC93 - 401116 - 424
12X-RAY DIFFRACTION6CO5011

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