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- PDB-6s1z: Crystal structure of Anopheles gambiae AnoACE2 in complex with fo... -

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Basic information

Entry
Database: PDB / ID: 6s1z
TitleCrystal structure of Anopheles gambiae AnoACE2 in complex with fosinoprilat
ComponentsAngiotensin-converting enzyme
KeywordsHYDROLASE / metalloprotease / mosquito control / insecticide design / fosinoprilat
Function / homology
Function and homology information


metallodipeptidase activity / Hydrolases; Acting on peptide bonds (peptidases) / peptidyl-dipeptidase activity / carboxypeptidase activity / metallopeptidase activity / proteolysis / extracellular space / zinc ion binding / plasma membrane
Similarity search - Function
Peptidase M2, peptidyl-dipeptidase A / Angiotensin-converting enzyme
Similarity search - Domain/homology
fosinoprilat / Angiotensin-converting enzyme
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCozier, G.E. / Acharya, K.R. / Cashman, J.S.
CitationJournal: Biochem.J. / Year: 2019
Title: Crystal structures of angiotensin-converting enzyme from Anopheles gambiae in its native form and with a bound inhibitor.
Authors: Cashman, J.S. / Cozier, G.E. / Harrison, C. / Isaac, R.E. / Acharya, K.R.
History
DepositionJun 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiotensin-converting enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1294
Polymers72,0411
Non-polymers1,0873
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint8 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.718, 166.718, 117.458
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-821-

HOH

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Components

#1: Protein Angiotensin-converting enzyme /


Mass: 72041.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: ANCE2, AgaP_AGAP009751 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: A0NFU8, Hydrolases; Acting on peptide bonds (peptidases)
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-KS8 / fosinoprilat / Fosinopril


Mass: 435.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34NO5P / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 43.2% v/v polypropylene glycol,30 mM sodium formate, 10 mM Tri pH 7.8, 0.3 % w/v gamma-PGA, 0.3% w/v PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→117.46 Å / Num. obs: 33809 / % possible obs: 100 % / Redundancy: 77.3 % / CC1/2: 1 / Rpim(I) all: 0.017 / Net I/σ(I): 24.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 79.8 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 3747 / CC1/2: 0.622 / Rpim(I) all: 0.137 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S1Y

6s1y


Resolution: 2.5→72.191 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.76 / Phase error: 39.13
RfactorNum. reflection% reflection
Rfree0.3365 1695 5.02 %
Rwork0.2939 --
obs0.2962 33760 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→72.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 70 25 4871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024983
X-RAY DIFFRACTIONf_angle_d0.4976762
X-RAY DIFFRACTIONf_dihedral_angle_d20.741851
X-RAY DIFFRACTIONf_chiral_restr0.035713
X-RAY DIFFRACTIONf_plane_restr0.002865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.57370.42231430.40352606X-RAY DIFFRACTION100
2.5737-2.65680.40751410.38452626X-RAY DIFFRACTION100
2.6568-2.75170.34721420.33652618X-RAY DIFFRACTION100
2.7517-2.86190.3621310.3322642X-RAY DIFFRACTION100
2.8619-2.99210.34141190.32512646X-RAY DIFFRACTION100
2.9921-3.14990.3591450.34132644X-RAY DIFFRACTION100
3.1499-3.34720.37351260.34642663X-RAY DIFFRACTION100
3.3472-3.60570.41911340.33442646X-RAY DIFFRACTION100
3.6057-3.96850.36931510.31142671X-RAY DIFFRACTION100
3.9685-4.54270.35351460.2892702X-RAY DIFFRACTION100
4.5427-5.72290.30611460.2652722X-RAY DIFFRACTION100
5.7229-72.22110.27871710.23252879X-RAY DIFFRACTION100

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