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- PDB-1j38: Crystal Structure of Drosophila AnCE -

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Basic information

Entry
Database: PDB / ID: 1j38
TitleCrystal Structure of Drosophila AnCE
Componentsangiotensin converting enzyme
KeywordsHYDROLASE / Angiotensin
Function / homology
Function and homology information


Metabolism of Angiotensinogen to Angiotensins / metamorphosis / response to symbiotic bacterium / peptidyl-dipeptidase A / sexual reproduction / peptide hormone processing / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / proteolysis ...Metabolism of Angiotensinogen to Angiotensins / metamorphosis / response to symbiotic bacterium / peptidyl-dipeptidase A / sexual reproduction / peptide hormone processing / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / proteolysis / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme / Peptidase family M2 domain profile. / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Angiotensin-converting enzyme
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsKim, H.M. / Shin, D.R. / Lee, H. / Lee, J.-O.
CitationJournal: Febs Lett. / Year: 2003
Title: Crystal structure of Drosophila angiotensin I-converting enzyme bound to captopril and lisinopril
Authors: Kim, H.M. / Shin, D.R. / Yoo, O.J. / Lee, H. / Lee, J.-O.
History
DepositionJan 20, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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_ref_seq_dif.details / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: angiotensin converting enzyme
B: angiotensin converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,0114
Polymers140,8802
Non-polymers1312
Water724
1
A: angiotensin converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5062
Polymers70,4401
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: angiotensin converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5062
Polymers70,4401
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.912, 121.223, 94.740
Angle α, β, γ (deg.)90.00, 99.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein angiotensin converting enzyme / AnCE


Mass: 70440.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q10714, peptidyl-dipeptidase A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.82 Å3/Da / Density % sol: 67.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium Formate 7.2M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120-25 mg/mlprotein1drop
220 mMHEPES1drop
30.2 M1droppH7.5NaCl
47.2 Msodium formate1reservoir
52 mM1reservoirZnCl2

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.928 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 22, 2000
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 71274 / Num. obs: 66143 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.7 Å / % possible all: 81.7
Reflection
*PLUS
Num. measured all: 442229 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 81.7 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.281 3307 random
Rwork0.246 --
all0.246 71274 -
obs0.246 66143 -
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9800 0 2 4 9806
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.008
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.5

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