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- PDB-2abz: Crystal structure of C19A/C43A mutant of leech carboxypeptidase i... -

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Basic information

Entry
Database: PDB / ID: 2abz
TitleCrystal structure of C19A/C43A mutant of leech carboxypeptidase inhibitor in complex with bovine carboxypeptidase A
Components
  • Carboxypeptidase A1
  • Metallocarboxypeptidase inhibitor
Keywordshydrolase/hydrolase inhibitor / inhibitor-metallocarboxypeptidase complex / LCI mutant / oxidative folding intermediate analog / hydrolase-hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


carboxypeptidase A / peptidase inhibitor activity / leukotriene metabolic process / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase inhibitor / Proteinase inhibitor I46, leech metallocarboxypeptidase inhibitor / Carboxypeptidase Inhibitor; Chain A / Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. ...Carboxypeptidase inhibitor / Proteinase inhibitor I46, leech metallocarboxypeptidase inhibitor / Carboxypeptidase Inhibitor; Chain A / Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxypeptidase A1 / Metallocarboxypeptidase inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsArolas, J.L. / Popowicz, G.M. / Bronsoms, S. / Aviles, F.X. / Huber, R. / Holak, T.A. / Ventura, S.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Study of a major intermediate in the oxidative folding of leech carboxypeptidase inhibitor: contribution of the fourth disulfide bond
Authors: Arolas, J.L. / Popowicz, G.M. / Bronsoms, S. / Aviles, F.X. / Huber, R. / Holak, T.A. / Ventura, S.
#1: Journal: NAT.STRUCT.MOL.BIOL. / Year: 2000
Title: Structure of a novel leech carboxypeptidase inhibitor determined free in solution and in complex with human carboxypeptidase A2
Authors: Reverter, D. / Fernandez-Catalan, C. / Baumgartner, R. / Pfander, R. / Huber, R. / Bode, W. / Vendrell, J. / Holak, T.A. / Aviles, F.X.
#2: Journal: Structure / Year: 2005
Title: NMR structural characterization and computational predictions of the major intermediate in oxidative folding of leech carboxypeptidase inhibitor
Authors: Arolas, J.L. / D'Silva, L. / Popowicz, G.M. / Aviles, F.X. / Holak, T.A. / Ventura, S.
History
DepositionJul 18, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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 A1
B: Carboxypeptidase A1
C: Metallocarboxypeptidase inhibitor
D: Metallocarboxypeptidase inhibitor
E: Metallocarboxypeptidase inhibitor
F: Metallocarboxypeptidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9078
Polymers98,7766
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.930, 124.930, 154.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Carboxypeptidase A1 / carboxypeptidase A / CPA / A/B metallocarboxypeptidase


Mass: 34721.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: P00730, carboxypeptidase A
#2: Protein
Metallocarboxypeptidase inhibitor / Leech carboxypeptidase inhibitor / LCI / inhibitor of A/B metallocarboxypeptidases


Mass: 7333.126 Da / Num. of mol.: 4 / Mutation: C19A/C43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Plasmid: pBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P81511
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5M Lithium Sulfate monohydrate, 100mM Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DetectorDate: Jun 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 66322

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Processing

SoftwareName: REFMAC / Version: 5.1.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.234 3360 RANDOM
Rwork0.189 --
all0.192 65785 -
obs0.19 62741 -
Refinement stepCycle: LAST / Resolution: 2.16→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 2 0 6504

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