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- PDB-4r5v: Structure of the m1 alanylaminopeptidase from malaria complexed w... -

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Basic information

Entry
Database: PDB / ID: 4r5v
TitleStructure of the m1 alanylaminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor
ComponentsM1 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / nucleus ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / nucleus / membrane / cytoplasm
Similarity search - Function
Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase, C-terminal domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold ...Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase, C-terminal domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-R5V / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum FcB1/Columbia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDrinkwater, N. / Mcgowan, S.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors.
Authors: Mistry, S.N. / Drinkwater, N. / Ruggeri, C. / Sivaraman, K.K. / Loganathan, S. / Fletcher, S. / Drag, M. / Paiardini, A. / Avery, V.M. / Scammells, P.J. / McGowan, S.
History
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Sep 20, 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 / 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M1 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,1196
Polymers104,4601
Non-polymers6585
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.222, 109.593, 118.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein M1 family aminopeptidase / Pfa-M1


Mass: 104460.492 Da / Num. of mol.: 1 / Fragment: UNP residues 195-1084
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum FcB1/Columbia (eukaryote)
Plasmid: PTRCHIS-2B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-R5V / N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}-2,2-dimethylpropanamide


Mass: 316.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N4O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% (v/v) PEG 8000, 10* (v/v) glycerol, 0.1 M Tris pH 8.5, 0.2 M MgCl2, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 13, 2014
RadiationMonochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→46.59 Å / Num. obs: 57652 / % possible obs: 99.5 % / Redundancy: 11.2 % / Biso Wilson estimate: 25.66 Å2 / Rmerge(I) obs: 0.201 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.1611.40.0132.2198.9
8.91-46.599.40.01348.1199.4

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.2.4data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
GDAdata collection
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EBG

3ebg


Resolution: 2.1→30.513 Å / SU ML: 0.24 / σ(F): 1.91 / Phase error: 20.78 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 2915 5.06 %5% of reflections
Rwork0.1811 ---
obs0.1832 57571 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7215 0 42 569 7826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037493
X-RAY DIFFRACTIONf_angle_d0.73710162
X-RAY DIFFRACTIONf_dihedral_angle_d13.6812818
X-RAY DIFFRACTIONf_chiral_restr0.0311123
X-RAY DIFFRACTIONf_plane_restr0.0031299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13440.26811470.25182531267899
2.1344-2.17120.27421480.24272547269599
2.1712-2.21070.32011440.22972525266998
2.2107-2.25320.28381160.230626072723100
2.2532-2.29920.27321380.22722540267898
2.2992-2.34920.28771410.2172580272199
2.3492-2.40380.23551330.219325722705100
2.4038-2.46390.28431190.21452573269299
2.4639-2.53050.26241440.20662559270399
2.5305-2.60490.22381460.20582598274499
2.6049-2.68890.23121290.19672585271499
2.6889-2.78490.25311390.19892584272399
2.7849-2.89640.26231460.19822602274899
2.8964-3.02810.27861390.185125932732100
3.0281-3.18760.20351280.189126042732100
3.1876-3.3870.2161430.170526222765100
3.387-3.64820.18441240.159826402764100
3.6482-4.01460.18631470.153126372784100
4.0146-4.59380.19481270.141126752802100
4.5938-5.78120.18351500.146727012851100
5.7812-30.51590.1821670.163327812948100
Refinement TLS params.Method: refined / Origin x: 17.6033 Å / Origin y: 3.831 Å / Origin z: 10.2029 Å
111213212223313233
T0.1475 Å20.0023 Å20.0159 Å2-0.1711 Å20.0166 Å2--0.1446 Å2
L0.5201 °2-0.2313 °20.0469 °2-1.3881 °20.4024 °2--0.9325 °2
S-0.0895 Å °-0.0477 Å °0.0471 Å °0.0402 Å °0.0339 Å °0.029 Å °-0.1256 Å °-0.0127 Å °0.0538 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA196 - 1084
2X-RAY DIFFRACTION1allA1 - 1101
3X-RAY DIFFRACTION1allA1 - 1102
4X-RAY DIFFRACTION1allA2 - 1769
5X-RAY DIFFRACTION1allA1 - 1105

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