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- PDB-4wz9: APN1 from Anopheles gambiae -

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Basic information

Entry
Database: PDB / ID: 4wz9
TitleAPN1 from Anopheles gambiae
Components
  • AGAP004809-PA
  • ALA-ALA-ALA-LYS-ALA
  • ALA-ALA-LYS
KeywordsHYDROLASE / aminopeptidase / metalloprotease
Function / homology
Function and homology information


peptide catabolic process / metalloaminopeptidase activity / peptide binding / proteolysis / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain ...Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / AGAP004809-PA
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
Drosophila (fruit flies)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å
AuthorsAtkinson, S.C. / Armistead, J.S. / Mathias, D.K. / Sandeu, M.M. / Tao, D. / Borhani-Dizaji, N. / Morlais, I. / Dinglasan, R.R. / Borg, N.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The Anopheles-midgut APN1 structure reveals a new malaria transmission-blocking vaccine epitope.
Authors: Atkinson, S.C. / Armistead, J.S. / Mathias, D.K. / Sandeu, M.M. / Tao, D. / Borhani-Dizaji, N. / Tarimo, B.B. / Morlais, I. / Dinglasan, R.R. / Borg, N.A.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Jul 15, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_keywords / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGAP004809-PA
B: AGAP004809-PA
M: ALA-ALA-ALA-LYS-ALA
N: ALA-ALA-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,47013
Polymers215,6084
Non-polymers8629
Water2,630146
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-94 kcal/mol
Surface area66070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.480, 132.900, 146.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 57 - 943 / Label seq-ID: 40 - 926

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AGAP004809-PA


Mass: 107443.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: AgaP_AGAP004809 / Production host: Drosophila (fruit flies) / References: UniProt: Q7Q2T8

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Protein/peptide , 2 types, 2 molecules MN

#2: Protein/peptide ALA-ALA-ALA-LYS-ALA


Mass: 431.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila (fruit flies) / Production host: Drosophila (fruit flies)
#3: Protein/peptide ALA-ALA-LYS


Mass: 289.351 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila (fruit flies) / Production host: Drosophila (fruit flies)

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Non-polymers , 5 types, 155 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#7: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: CHES, PEG 8000 / PH range: pH 9.7

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 64356 / % possible obs: 99.5 % / Redundancy: 8.8 % / Net I/σ(I): 13.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementStarting model: PDB ENTRY 4FKE

4fke


Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 27.723 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 1.046 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2538 3256 5.1 %RANDOM
Rwork0.20001 ---
obs0.20275 61048 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.546 Å2
Baniso -1Baniso -2Baniso -3
1--4.5 Å20 Å2-0 Å2
2--3.09 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14113 0 46 146 14305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914483
X-RAY DIFFRACTIONr_bond_other_d0.0050.0213444
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.93819712
X-RAY DIFFRACTIONr_angle_other_deg1.071330745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.06651772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31523.892704
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.203152310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5381596
X-RAY DIFFRACTIONr_chiral_restr0.0830.22201
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216617
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023555
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7064.0197103
X-RAY DIFFRACTIONr_mcbond_other2.7054.0187102
X-RAY DIFFRACTIONr_mcangle_it4.1546.0228870
X-RAY DIFFRACTIONr_mcangle_other4.1546.0238871
X-RAY DIFFRACTIONr_scbond_it3.064.267380
X-RAY DIFFRACTIONr_scbond_other3.064.2617381
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7856.28710843
X-RAY DIFFRACTIONr_long_range_B_refined7.91238.2864192
X-RAY DIFFRACTIONr_long_range_B_other7.91238.28164193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 53028 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 236 -
Rwork0.309 4418 -
obs--98.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6210.720.15670.47560.00770.6050.1925-0.00630.44130.0859-0.06360.2287-0.0692-0.0139-0.12890.04620.01310.09160.0449-0.01180.225925.275-14.1102-5.9902
20.7154-0.3154-0.41930.95260.66490.92130.0960.01640.0912-0.07110.0066-0.1866-0.0042-0.0605-0.10270.05570.02230.03370.03970.00530.044541.864-52.3317-43.5445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 943
2X-RAY DIFFRACTION2B57 - 943

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