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- PDB-1jqg: Crystal Structure of the Carboxypeptidase A from Helicoverpa Armigera -

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Basic information

Entry
Database: PDB / ID: 1jqg
TitleCrystal Structure of the Carboxypeptidase A from Helicoverpa Armigera
Componentscarboxypeptidase A
KeywordsHYDROLASE / PRO-PROTEIN
Function / homology
Function and homology information


carboxypeptidase A / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Metallocarboxypeptidase-like / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...Metallocarboxypeptidase-like / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicoverpa armigera (cotton bollworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEstebanez-Perpina, E. / Bayes, A. / Vendrell, J. / Jongsma, M.A. / Bown, D.P. / Gatehouse, J.A. / Huber, R. / Bode, W. / Aviles, F.X. / Reverter, D.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of a novel mid-gut procarboxypeptidase from the cotton pest Helicoverpa armigera.
Authors: Estebanez-Perpina, E. / Bayes, A. / Vendrell, J. / Jongsma, M.A. / Bown, D.P. / Gatehouse, J.A. / Huber, R. / Bode, W. / Aviles, F.X. / Reverter, D.
#1: Journal: Insect Biochem.Mol.Biol. / Year: 1998
Title: Midgut carboxypeptidase from Helicoverpa armigera (Lepidoptera: Noctuidae) larvae: enzyme characterisation, cDNA cloning and expression.
Authors: Bown, D.P. / Wilkinson, H.S. / Gatehouse, J.A.
History
DepositionAug 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: carboxypeptidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6042
Polymers48,5391
Non-polymers651
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.03, 86.39, 50.55
Angle α, β, γ (deg.)90, 100.70, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein carboxypeptidase A / procarboxypeptidase A


Mass: 48539.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicoverpa armigera (cotton bollworm) / Tissue: MIDGUT / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: O97389, carboxypeptidase A
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: PEG 8000, Na-Acetate, Na-Cacodylate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Method: unknown / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMTris-HCl11pH8.0
20.001 mM11ZnCl2
310 mg/mlprotein11
430 %(w/v)PEG800012
50.2 Msodium acetate12
60.1 Msodium cacodylate12pH5.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 16, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 230224 / Num. obs: 21449 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.034 / Mean I/σ(I) obs: 2.5 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 12 Å / Num. measured all: 230224
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.344

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AYE

1aye


Resolution: 2.5→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2381 981 -RANDOM
Rwork0.1801 ---
all0.1801 230224 --
obs0.18 18816 93.2 %-
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 1 157 3387
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.6
LS refinement shellResolution: 2.5→2.6 Å
RfactorNum. reflection
Rfree0.227 61
Rwork0.187 -
obs-1394
Refinement
*PLUS
Lowest resolution: 12 Å / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.5

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