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- PDB-3d68: Crystal structure of a T325I/T329I/H333Y/H335Q mutant of Thrombin... -

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Basic information

Entry
Database: PDB / ID: 3d68
TitleCrystal structure of a T325I/T329I/H333Y/H335Q mutant of Thrombin-Activatable Fibrinolysis Inhibitor (TAFI-IIYQ)
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 / Metabolism of Angiotensinogen to Angiotensins / negative regulation of fibrinolysis / metallocarboxypeptidase activity / fibrinolysis / liver regeneration / Regulation of Complement cascade ...carboxypeptidase U / positive regulation of extracellular matrix constituent secretion / negative regulation of hepatocyte proliferation / negative regulation of plasminogen activation / Metabolism of Angiotensinogen to Angiotensins / negative regulation of fibrinolysis / metallocarboxypeptidase activity / fibrinolysis / liver regeneration / Regulation of Complement cascade / 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 / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases ...Carboxypeptidase B2 / Metallocarboxypeptidase-like / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Peptidase family M14 domain profile. / Zn_pept / 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
ARGININE / Carboxypeptidase B2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id ..._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

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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)149,27920
Polymers146,1233
Non-polymers3,15517
Water0
1
A: Carboxypeptidase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8337
Polymers48,7081
Non-polymers1,1256
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carboxypeptidase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8337
Polymers48,7081
Non-polymers1,1256
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Carboxypeptidase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6126
Polymers48,7081
Non-polymers9045
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.460, 159.460, 139.180
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
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 1 - 650 / Label seq-ID: 24

Dom-IDAuth asym-IDLabel asym-ID
1AA - I
2BB - O
3CC - T

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Components

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


Mass: 48707.805 Da / Num. of mol.: 3 / Fragment: TAFI-IIYQ, UNP residues 24-423 / Mutation: T325I, T329I, H333Y, H335Q
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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 11
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
#4: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N4O2
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: 3.5 Å3/Da / Density % sol: 64.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 16-18% PEG 3000, 0.18-0.22mM Na/K-tartrate, 50mM L-glutamate, 50mM 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: ID23-1 / Wavelength: 0.97295 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97295 Å / Relative weight: 1
ReflectionResolution: 2.8→49.03 Å / Num. all: 50676 / Num. obs: 50644 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 4.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0008refinement
XDSdata scaling
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3D66

3d66


Resolution: 2.8→49.03 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 29.163 / SU ML: 0.248 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.585 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23156 2582 5.1 %RANDOM
Rwork0.18755 ---
obs0.18976 48058 99.97 %-
all-48058 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.601 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å21.27 Å20 Å2
2--2.53 Å20 Å2
3----3.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9747 0 193 0 9940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02210215
X-RAY DIFFRACTIONr_bond_other_d0.0020.026865
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.94913890
X-RAY DIFFRACTIONr_angle_other_deg1.0273.00216574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.30751200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55723.5480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.436151668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9741560
X-RAY DIFFRACTIONr_chiral_restr0.1080.21520
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022163
X-RAY DIFFRACTIONr_nbd_refined0.2460.22414
X-RAY DIFFRACTIONr_nbd_other0.2060.27107
X-RAY DIFFRACTIONr_nbtor_refined0.2090.24982
X-RAY DIFFRACTIONr_nbtor_other0.1030.25458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2204
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0660.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1030.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9241.57631
X-RAY DIFFRACTIONr_mcbond_other0.1281.52426
X-RAY DIFFRACTIONr_mcangle_it1.11929750
X-RAY DIFFRACTIONr_scbond_it1.53935042
X-RAY DIFFRACTIONr_scangle_it2.2654.54140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5585 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.460.5
2Bmedium positional0.490.5
3Cmedium positional0.410.5
1Amedium thermal2.98
2Bmedium thermal4.01
3Cmedium thermal2.76
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 193 -
Rwork0.347 3489 -
obs--99.97 %
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)
16.06140.30662.5113.76361.39836.43720.0541-0.35350.63870.0557-0.2094-0.4513-0.48550.12520.15530.1123-0.0431-0.1735-0.20910.106-0.169344.764355.309550.5661
22.2361-0.31851.58742.5961.11395.96940.1702-0.14450.01660.054-0.283-0.1740.4786-0.41640.1127-0.18230.017-0.0918-0.29590.093-0.30833.443336.391237.6867
35.13811.1337-2.19014.1479-0.84725.1373-0.06160.3061-0.115-0.00530.1398-0.68890.51080.3943-0.07820.11510.2910.0399-0.12780.0735-0.003766.91-15.711411.8044
42.8572-0.4731-0.96993.5308-0.65664.74150.0162-0.12460.03780.1345-0.0193-0.21370.3075-0.30590.0031-0.1490.07330.0369-0.33850.1323-0.367247.5176-5.078324.4376
52.96891.247-1.11684.976-1.98134.6747-0.06740.34640.3452-0.1421-0.1166-0.8155-0.17510.69030.184-0.17420.10760.04040.39180.34470.238563.697936.6268-16.129
62.4072-0.7692-0.26172.6039-1.00864.1198-0.1272-0.02060.2213-0.0123-0.183-0.32110.05630.15160.3102-0.37230.17430.0185-0.24240.1475-0.234442.07629.4954-5.1667
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 DIFFRACTION2AO5011
5X-RAY DIFFRACTION3BB1 - 9224 - 115
6X-RAY DIFFRACTION3BH - K601 - 6041
7X-RAY DIFFRACTION4BB93 - 401116 - 424
8X-RAY DIFFRACTION4BP5011
9X-RAY DIFFRACTION5CC1 - 9224 - 115
10X-RAY DIFFRACTION5CL - N601 - 6041
11X-RAY DIFFRACTION6CC93 - 401116 - 424
12X-RAY DIFFRACTION6CQ5011

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