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- PDB-3fju: Ascaris suum carboxypeptidase inhibitor in complex with human car... -

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Basic information

Entry
Database: PDB / ID: 3fju
TitleAscaris suum carboxypeptidase inhibitor in complex with human carboxypeptidase A1
Components(Carboxypeptidase ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Ascariasis / host resistance / metallocarboxypeptidase inhibitor / immunolocalization / Carboxypeptidase / Hydrolase / Metal-binding / Metalloprotease / Protease / Secreted / Zymogen / Metalloenzyme inhibitor / Metalloprotease inhibitor / Protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


carboxypeptidase A / metalloendopeptidase inhibitor activity / leukotriene metabolic process / metallocarboxypeptidase activity / response to cadmium ion / proteolysis involved in protein catabolic process / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Herpes Virus-1 - #170 / Ascaris metallocarboxypeptidase inhibitor / : / Metallo-carboxypeptidase inhibitor / 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. ...Herpes Virus-1 - #170 / Ascaris metallocarboxypeptidase inhibitor / : / Metallo-carboxypeptidase inhibitor / 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. / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Herpes Virus-1 / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / Carboxypeptidase A1 / Carboxypeptidase A inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
Ascaris suum (pig roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSanglas, L. / Aviles, F.X. / Huber, R. / Gomis-Ruth, F.X. / Arolas, J.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Mammalian metallopeptidase inhibition at the defense barrier of Ascaris parasite
Authors: Sanglas, L. / Aviles, F.X. / Huber, R. / Gomis-Ruth, F.X. / Arolas, J.L.
History
DepositionDec 15, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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 A1
B: Carboxypeptidase A inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,55423
Polymers41,9742
Non-polymers1,57921
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-302 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.470, 78.700, 84.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Carboxypeptidase ... , 2 types, 2 molecules AB

#1: Protein Carboxypeptidase A1


Mass: 34470.586 Da / Num. of mol.: 1 / Fragment: UNP residues 112-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPA1, CPA / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: P15085, carboxypeptidase A
#2: Protein Carboxypeptidase A inhibitor


Mass: 7503.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris suum (pig roundworm) / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 Origami2 / References: UniProt: P19399

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Non-polymers , 5 types, 585 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE DATABASE OF ENTITY 2 (UNP 19399, ICAA_ASCSU) IS INCORRECT. THE C-TERMINAL 61-65 ...THE SEQUENCE DATABASE OF ENTITY 2 (UNP 19399, ICAA_ASCSU) IS INCORRECT. THE C-TERMINAL 61-65 RESIDUES LPWGL SHOULD BE GCCWDLL (61-67).

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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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x3-well CrystalQuick plates (Greiner) by a Cartesian nanodrop robot (Genomic Solutions) ...Details: Reservoir solutions were prepared by a Tecan robot and 200-nL crystallization drops were dispensed on 96x3-well CrystalQuick plates (Greiner) by a Cartesian nanodrop robot (Genomic Solutions) at the joint IBMB-CSIC/IRB/Barcelona Science Park High-Throughput Crystallography Platform (PAC). Best crystals appeared after 2-3 weeks in a Bruker steady-temperature crystal farm at 20 C with 0.2 M zinc acetate dihydrate, 0.1 M sodium cacodylate, 9% PEG 8000, pH 6.5 as reservoir solution. These conditions were successfully scaled up to the microliter range with Cryschem crystallization dishes (Hampton Research) using drops containing 3 microl of protein solution (16.5 mg/ml) and 1 microl of reservoir solution, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→46.4 Å / Num. obs: 49284 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 18.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 4.6 / Num. unique all: 6967 / % possible all: 97.7

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Processing

Software
NameVersionClassification
ProDCdata collection
AMoREphasing
REFMAC5.5.0046refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V77

2v77


Resolution: 1.6→46.37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.193 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20025 752 1.5 %RANDOM
Rwork0.15706 ---
all0.15769 49798 --
obs0.15769 48532 99.55 %-
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: 12.229 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 55 564 3573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2971.9424187
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75524.317139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94915505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.371512
X-RAY DIFFRACTIONr_chiral_restr0.0910.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212325
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8941.51870
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.32323019
X-RAY DIFFRACTIONr_scbond_it2.17731211
X-RAY DIFFRACTIONr_scangle_it3.0044.51168
X-RAY DIFFRACTIONr_rigid_bond_restr1.25733081
X-RAY DIFFRACTIONr_sphericity_free4.6853577
X-RAY DIFFRACTIONr_sphericity_bonded2.36233010
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 51 -
Rwork0.159 3379 -
obs--95.25 %

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