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- PDB-4a94: Structure of the carboxypeptidase inhibitor from Nerita versicolo... -

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Basic information

Entry
Database: PDB / ID: 4a94
TitleStructure of the carboxypeptidase inhibitor from Nerita versicolor in complex with human CPA4
Components
  • CARBOXYPEPTIDASE A4
  • CARBOXYPEPTIDASE INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / CPA4 / NVCI / PCI / LCI
Function / homology
Function and homology information


: / metalloendopeptidase inhibitor activity / negative regulation of endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding / metal ion binding
Similarity search - Function
Laminin - #90 / 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 ...Laminin - #90 / 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 / Laminin / Aminopeptidase / Ribbon / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Metallocarboxypeptidase inhibitor / Carboxypeptidase A4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
NERITA VERSICOLOR (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCovaleda, G. / Alonso, M. / Chavez, M.A. / Aviles, F.X. / Reverter, D.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of a Novel Metallo-Carboxypeptidase Inhibitor from the Marine Mollusk Nerita Versicolor in Complex with Human Carboxypeptidase A4.
Authors: Covaleda, G. / Alonso Del Rivero, M. / Chavez, M.A. / Aviles, F.X. / Reverter, D.
History
DepositionNov 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Mar 28, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A4
B: CARBOXYPEPTIDASE A4
C: CARBOXYPEPTIDASE INHIBITOR
D: CARBOXYPEPTIDASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,11812
Polymers81,6154
Non-polymers5038
Water5,459303
1
A: CARBOXYPEPTIDASE A4
D: CARBOXYPEPTIDASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0596
Polymers40,8082
Non-polymers2514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-41 kcal/mol
Surface area14110 Å2
MethodPISA
2
B: CARBOXYPEPTIDASE A4
C: CARBOXYPEPTIDASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0596
Polymers40,8082
Non-polymers2514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-38.9 kcal/mol
Surface area13830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.220, 71.980, 79.840
Angle α, β, γ (deg.)90.00, 108.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CARBOXYPEPTIDASE A4 / CARBOXYPEPTIDASE A3


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


Mass: 5956.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NERITA VERSICOLOR (invertebrata) / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: P86912*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.3 Å3/Da / Density % sol: 46.54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→48.33 Å / Num. obs: 79658 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 17.25 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.4
Reflection shellResolution: 1.7→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.8 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.093 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 3979 5 %
Rwork0.2054 --
obs0.2068 79607 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.369 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.345 Å2-0 Å2-2.2878 Å2
2---0.5003 Å20 Å2
3----3.8448 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5574 0 26 303 5903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075758
X-RAY DIFFRACTIONf_angle_d1.0337818
X-RAY DIFFRACTIONf_dihedral_angle_d15.0372022
X-RAY DIFFRACTIONf_chiral_restr0.075820
X-RAY DIFFRACTIONf_plane_restr0.0051028
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.76080.30663450.2676317X-RAY DIFFRACTION82
1.7608-1.83130.29733910.24627205X-RAY DIFFRACTION94
1.8313-1.91470.2494060.21717704X-RAY DIFFRACTION100
1.9147-2.01560.25063760.20757742X-RAY DIFFRACTION100
2.0156-2.14190.23653960.20077737X-RAY DIFFRACTION100
2.1419-2.30730.23754490.19937728X-RAY DIFFRACTION100
2.3073-2.53950.23584010.19577722X-RAY DIFFRACTION100
2.5395-2.90690.23274250.21037782X-RAY DIFFRACTION100
2.9069-3.66210.24013990.20887805X-RAY DIFFRACTION100
3.6621-46.10990.18683910.17987886X-RAY DIFFRACTION100

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