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- PDB-1zlh: Crystal structure of the tick carboxypeptidase inhibitor in compl... -

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Basic information

Entry
Database: PDB / ID: 1zlh
TitleCrystal structure of the tick carboxypeptidase inhibitor in complex with bovine carboxypeptidase A
Components
  • Carboxypeptidase A1
  • carboxypeptidase inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor-metallocarboxypeptidase complex / beta-defensin fold (TCI) / eight-stranded twisted beta-sheet surrounded by eight alpha-helices (CPA) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


carboxypeptidase A / acquisition of nutrients from host / metalloendopeptidase inhibitor activity / leukotriene metabolic process / enzyme inhibitor activity / metallocarboxypeptidase activity / toxin activity / proteolysis / extracellular space / extracellular region / zinc ion binding
Similarity search - Function
Carboxypeptidase inhibitor, N-terminal domain / Carboxypeptidase inhibitor I68 / Carboxypeptidase inhibitor I68 / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Carboxypeptidase A, carboxypeptidase domain / 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 / Anthopleurin-A / Myotoxin/Anemone neurotoxin domain superfamily / Anthopleurin-A / Carboxypeptidase A, carboxypeptidase domain / ligand-binding face of the semaphorins, domain 2 / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / 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
: / Carboxypeptidase A1 / Carboxypeptidase inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Rhipicephalus bursa (arthropod)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.7 Å
AuthorsArolas, J.L. / Popowicz, G.M. / Lorenzo, J. / Sommerhoff, C.P. / Huber, R. / Aviles, F.X. / Holak, T.A.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: The Three-Dimensional Structures of Tick Carboxypeptidase Inhibitor in Complex with A/B Carboxypeptidases Reveal a Novel Double-headed Binding Mode
Authors: Arolas, J.L. / Popowicz, G.M. / Lorenzo, J. / Sommerhoff, C.P. / Huber, R. / Aviles, F.X. / Holak, T.A.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: A carboxypeptidase inhibitor from the tick Rhipicephalus bursa: isolation, cDNA cloning, recombinant expression, and characterization
Authors: Arolas, J.L. / Lorenzo, J. / Rovira, A. / Castella, J. / Aviles, F.X. / Sommerhoff, C.P.
History
DepositionMay 6, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 13, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9947
Polymers42,6672
Non-polymers3275
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-131 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.070, 68.600, 57.890
Angle α, β, γ (deg.)90.00, 104.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 34721.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: P00730, carboxypeptidase A
#2: Protein carboxypeptidase inhibitor / inhibitor of A/B metallocarboxypeptidases


Mass: 7945.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhipicephalus bursa (arthropod) / Plasmid: pBAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 58374130, UniProt: Q5EPH2*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O
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: 2.1 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M sodium cacodylate, 0.2M zinc acetate dihydrate, 7%(w/v) PEG 8000, 10%(w/v) dried dioxan, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 7, 2004 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.67→30 Å / Num. all: 39265 / Num. obs: 34176 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.67→1.8 Å / Rmerge(I) obs: 0.134 / Num. unique all: 3786 / % possible all: 61.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MIR / Resolution: 1.7→55.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.988 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.225 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18532 1832 5.1 %RANDOM
Rwork0.15403 ---
all0.1597 39265 --
obs0.15561 34435 92.44 %-
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: 12.551 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20.24 Å2
2---0.26 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.7→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 5 379 3285
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212981
X-RAY DIFFRACTIONr_bond_other_d0.0020.022569
X-RAY DIFFRACTIONr_angle_refined_deg1.121.944048
X-RAY DIFFRACTIONr_angle_other_deg0.77835992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6315372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0640.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023343
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02624
X-RAY DIFFRACTIONr_nbd_refined0.1920.2642
X-RAY DIFFRACTIONr_nbd_other0.240.23108
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0230.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4671.51854
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84322976
X-RAY DIFFRACTIONr_scbond_it1.11831127
X-RAY DIFFRACTIONr_scangle_it1.7634.51072
X-RAY DIFFRACTIONr_rigid_bond_restr0.61822981
X-RAY DIFFRACTIONr_sphericity_free1.3092384
X-RAY DIFFRACTIONr_sphericity_bonded0.62622903
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 68
Rwork0.234 1446

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