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- PDB-7eqx: Crystal structure of an Aedes aegypti procarboxypeptidase B1 -

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Basic information

Entry
Database: PDB / ID: 7eqx
TitleCrystal structure of an Aedes aegypti procarboxypeptidase B1
Components(Carboxypeptidase B) x 2
KeywordsHYDROLASE / Procarboxypeptidase B1 / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


carboxypeptidase B / metallocarboxypeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase
Similarity search - Domain/homology
Biological speciesAedes aegypti (yellow fever mosquito)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsChoong, Y.K. / Gavor, E. / Jobichen, C. / Sivaraman, J.
CitationJournal: Life Sci Alliance / Year: 2022
Title: Structure of Aedes aegypti procarboxypeptidase B1 and its binding with Dengue virus for controlling infection.
Authors: Gavor, E. / Choong, Y.K. / Tulsian, N.K. / Nayak, D. / Idris, F. / Sivaraman, H. / Ting, D.H.R. / Sylvie, A. / Mok, Y.K. / Kini, R.M. / Sivaraman, J.
History
DepositionMay 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxypeptidase B
B: Carboxypeptidase B
C: Carboxypeptidase B
D: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7366
Polymers88,6054
Non-polymers1312
Water11,872659
1
A: Carboxypeptidase B
C: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3683
Polymers44,3022
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxypeptidase B
D: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3683
Polymers44,3022
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.797, 74.436, 83.108
Angle α, β, γ (deg.)90.00, 119.08, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid -1 or (resid 0 and (name...
d_2ens_1(chain "B" and ((resid -1 through 1 and (name N...
d_1ens_2(chain "C" and (resid 7 through 27 or (resid 28...
d_2ens_2(chain "D" and ((resid 7 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLYA1 - 80
d_21ens_1PROGLYB1 - 80
d_11ens_2ASPPHEC1 - 299
d_21ens_2ASPPHED1 - 299

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.406232472654, 0.415435422762, -0.813872586881), (0.414912948591, -0.87742437383, -0.240777310602), (-0.814139068743, -0.239874712555, -0.528807809155)29.1292753264, 89.732669784, 95.5627927792
2given(0.376494530634, 0.420088836028, -0.82569803091), (0.4041187175, -0.876482802134, -0.261660007889), (-0.833630571997, -0.235166467438, -0.49975674285)31.0034539565, 89.9692556675, 95.8126448687

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Components

#1: Protein Carboxypeptidase B


Mass: 11371.806 Da / Num. of mol.: 2 / Fragment: Pro-region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: CPB-I / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q6J661, carboxypeptidase B
#2: Protein Carboxypeptidase B


Mass: 32930.691 Da / Num. of mol.: 2 / Fragment: Mature region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: CPB-I / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q6J661, carboxypeptidase B
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulphate, 0.1M sodium cacodylate trihydrate pH 6.5, 30% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 44087 / % possible obs: 98.4 % / Redundancy: 5 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.067 / Net I/σ(I): 27.74
Reflection shellResolution: 2.08→2.16 Å / Num. unique obs: 2867 / Rsym value: 0.159

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JQG

1jqg


Resolution: 2.08→33.63 Å / SU ML: 0.178 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.649
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.198 2000 4.54 %
Rwork0.168 --
obs0.169 44085 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.77 Å2
Refinement stepCycle: LAST / Resolution: 2.08→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5902 0 2 659 6563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036056
X-RAY DIFFRACTIONf_angle_d0.6268240
X-RAY DIFFRACTIONf_dihedral_angle_d5.597822
X-RAY DIFFRACTIONf_chiral_restr0.045887
X-RAY DIFFRACTIONf_plane_restr0.0051067
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.93347989605
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS0.57802784902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.24071360.17962867X-RAY DIFFRACTION95
2.13-2.190.24511410.1682967X-RAY DIFFRACTION97
2.19-2.260.2021400.16892936X-RAY DIFFRACTION98
2.26-2.330.21831420.16762988X-RAY DIFFRACTION98
2.33-2.410.21991410.16982976X-RAY DIFFRACTION98
2.41-2.510.21111410.17352974X-RAY DIFFRACTION99
2.51-2.620.20641440.17473013X-RAY DIFFRACTION98
2.62-2.760.23561410.18132987X-RAY DIFFRACTION99
2.76-2.930.22131450.18443040X-RAY DIFFRACTION99
2.93-3.160.19681440.17233019X-RAY DIFFRACTION99
3.16-3.480.2011450.1693055X-RAY DIFFRACTION100
3.48-3.980.18571450.15073057X-RAY DIFFRACTION100
3.98-5.010.15261460.14333062X-RAY DIFFRACTION100
5.01-33.630.18391490.18463144X-RAY DIFFRACTION100

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