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- PDB-4bd9: Structure of the complex between SmCI and human carboxypeptidase A4 -

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Basic information

Entry
Database: PDB / ID: 4bd9
TitleStructure of the complex between SmCI and human carboxypeptidase A4
Components
  • CARBOXYPEPTIDASE A4
  • CARBOXYPEPTIDASE INHIBITOR SMCI
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / SERINE PROTEASE INHIBITOR
Function / homology
Function and homology information


metalloendopeptidase inhibitor activity / hormone catabolic process / peptide catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / serine-type endopeptidase inhibitor activity / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
Tissue factor pathway inhibitor-like / 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 ...Tissue factor pathway inhibitor-like / 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 / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Zn peptidases / Aminopeptidase / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxypeptidase inhibitor SmCI / Carboxypeptidase A4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SABELLASTARTE MAGNIFICA (feather duster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAlonso-del-Ribero, M. / Reytor, M.L. / Trejo, S.A. / Chavez, M.A. / Aviles, F.X. / Reverter, D.
CitationJournal: Structure / Year: 2013
Title: A Noncanonical Mechanism of Carboxypeptidase Inhibition Revealed by the Crystal Structure of the Tri-Kunitz Smci in Complex with Human Cpa4.
Authors: Alonso Del Rivero, M. / Reytor, M.L. / Trejo, S.A. / Chavez, M.A. / Aviles, F.X. / Reverter, D.
History
DepositionOct 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A4
B: CARBOXYPEPTIDASE INHIBITOR SMCI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5413
Polymers53,4762
Non-polymers651
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-46.2 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.670, 138.670, 161.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2006-

HOH

21A-2024-

HOH

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Components

#1: Protein CARBOXYPEPTIDASE A4 / CARBOXYPEPTIDASE A3


Mass: 34851.031 Da / Num. of mol.: 1 / Fragment: RESIDUES 112-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZAA / Production host: KOMAGATAELLA PASTORIS (fungus)
References: UniProt: Q9UI42, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases
#2: Protein CARBOXYPEPTIDASE INHIBITOR SMCI / SMCI INHIBITOR


Mass: 18624.600 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SABELLASTARTE MAGNIFICA (feather duster)
Plasmid: PPICZAA / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: P84875
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.66 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97626
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.1→48.18 Å / Num. obs: 53712 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 32.68 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A94 CHAIN A

4a94


Resolution: 2.2→38.856 Å / SU ML: 0.31 / σ(F): 1.33 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2538 2365 5.1 %
Rwork0.2231 --
obs0.2247 46623 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.176 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0966 Å20 Å20 Å2
2--3.0966 Å20 Å2
3----6.1933 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3705 0 1 123 3829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083817
X-RAY DIFFRACTIONf_angle_d1.1335165
X-RAY DIFFRACTIONf_dihedral_angle_d18.1791350
X-RAY DIFFRACTIONf_chiral_restr0.078527
X-RAY DIFFRACTIONf_plane_restr0.005685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27870.33312250.28134269X-RAY DIFFRACTION98
2.2787-2.36990.29472330.27184379X-RAY DIFFRACTION100
2.3699-2.47770.33422450.27364381X-RAY DIFFRACTION100
2.4777-2.60830.34292190.28114413X-RAY DIFFRACTION100
2.6083-2.77170.29552690.26214368X-RAY DIFFRACTION100
2.7717-2.98570.27822520.26784387X-RAY DIFFRACTION100
2.9857-3.2860.29952110.24254495X-RAY DIFFRACTION100
3.286-3.76110.23172350.21054482X-RAY DIFFRACTION100
3.7611-4.73730.18812300.16974540X-RAY DIFFRACTION100
4.7373-38.86170.21162460.18564544X-RAY DIFFRACTION95

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