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- PDB-6ea1: X-ray crystal structure of Pf-M1 in complex with inhibitor (6da) ... -

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Basic information

Entry
Database: PDB / ID: 6ea1
TitleX-ray crystal structure of Pf-M1 in complex with inhibitor (6da) and catalytic zinc ion
ComponentsM1 family aminopeptidase
Keywordshydrolase/hydrolase inhibitor / M1 ALANYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / HYDROLASE / 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 / membrane ...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 / membrane / nucleus / cytoplasm
Similarity search - Function
Peptidase M1, alanyl aminopeptidase, C-terminal domain / Aminopeptidase N, middle-beta 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 ...Peptidase M1, alanyl aminopeptidase, C-terminal domain / Aminopeptidase N, middle-beta 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-J0Y / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.815 Å
AuthorsDrinkwater, N. / McGowan, S.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1063786 Australia
Australian Research Council (ARC)FT100100690 Australia
CitationJournal: J. Med. Chem. / Year: 2019
Title: Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases.
Authors: Vinh, N.B. / Drinkwater, N. / Malcolm, T.R. / Kassiou, M. / Lucantoni, L. / Grin, P.M. / Butler, G.S. / Duffy, S. / Overall, C.M. / Avery, V.M. / Scammells, P.J. / McGowan, S.
History
DepositionAug 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)104,67912
Polymers103,6321
Non-polymers1,04711
Water21,5101194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.491, 108.920, 118.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein M1 family aminopeptidase / Pfa-M1


Mass: 103631.609 Da / Num. of mol.: 1 / Fragment: UNP residues 195 to 1084 / Mutation: N213Q, N223Q, H378P, N501Q, N745Q, N795Q, N1069Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate FcB1 / Columbia) (eukaryote)
Strain: isolate FcB1 / Columbia / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Non-polymers , 5 types, 1205 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-J0Y / (2R)-2,3,3,3-tetrafluoro-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]propanamide


Mass: 424.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H11F7N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1194 / 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: 47.52 % / Mosaicity: 0.62 °
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

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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: Jul 13, 2016
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: 1.81→54.93 Å / Num. obs: 88426 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.99 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.07 / Rrim(I) all: 0.187 / Net I/σ(I): 8.7 / Num. measured all: 612689 / Scaling rejects: 141
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.81-1.855.61.2372491344160.4970.5561.3611.498.3
9.77-54.935.70.09537856640.9910.0410.1042299.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimless0.5.9data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.815→54.46 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2014 4450 5.04 %
Rwork0.1572 83898 -
obs0.1594 88348 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.07 Å2 / Biso mean: 19.0335 Å2 / Biso min: 6.22 Å2
Refinement stepCycle: final / Resolution: 1.815→54.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7247 0 64 1194 8505
Biso mean--27.12 31.11 -
Num. residues----889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017538
X-RAY DIFFRACTIONf_angle_d1.16710216
X-RAY DIFFRACTIONf_chiral_restr0.0521123
X-RAY DIFFRACTIONf_plane_restr0.0061306
X-RAY DIFFRACTIONf_dihedral_angle_d13.5362844
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.815-1.83560.32641180.27282752287098
1.8356-1.85720.28441480.26522679282798
1.8572-1.87990.31661400.25662773291399
1.8799-1.90370.30931370.23662741287899
1.9037-1.92870.28111530.21942745289899
1.9287-1.95510.25431490.21182744289399
1.9551-1.98310.25461450.196728072952100
1.9831-2.01270.2591380.187427402878100
2.0127-2.04410.21691440.186227972941100
2.0441-2.07760.24081670.17327202887100
2.0776-2.11350.20571690.168827822951100
2.1135-2.15190.18331590.157627652924100
2.1519-2.19330.22561570.157527752932100
2.1933-2.23810.2191330.156527822915100
2.2381-2.28670.19261450.158227902935100
2.2867-2.33990.22871450.163128002945100
2.3399-2.39840.20731450.157727972942100
2.3984-2.46330.22261320.150628122944100
2.4633-2.53580.21351590.150727722931100
2.5358-2.61760.20161600.158728022962100
2.6176-2.71120.21131470.154728022949100
2.7112-2.81970.21761470.158628332980100
2.8197-2.9480.21341530.151427962949100
2.948-3.10340.18051530.146328032956100
3.1034-3.29790.19331390.139328402979100
3.2979-3.55240.15271320.131928382970100
3.5524-3.90990.14981510.124328523003100
3.9099-4.47540.17651500.11928533003100
4.4754-5.63760.14451550.122529043059100
5.6376-54.48450.18011800.16430023182100
Refinement TLS params.Method: refined / Origin x: -17.6159 Å / Origin y: 4.1529 Å / Origin z: -10.351 Å
111213212223313233
T0.0709 Å20.0065 Å20.0069 Å2-0.0863 Å2-0.0107 Å2--0.0741 Å2
L0.335 °20.1336 °20.0057 °2-0.6508 °2-0.1072 °2--0.4672 °2
S-0.0313 Å °0.0064 Å °0.0306 Å °0.0008 Å °0.0102 Å °0.0133 Å °-0.0308 Å °0.0006 Å °0.0207 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA196 - 1084
2X-RAY DIFFRACTION1allB1001
3X-RAY DIFFRACTION1allB2001
4X-RAY DIFFRACTION1allB4 - 5
5X-RAY DIFFRACTION1allC1 - 3
6X-RAY DIFFRACTION1allC6
7X-RAY DIFFRACTION1allS3 - 1246
8X-RAY DIFFRACTION1allD1
9X-RAY DIFFRACTION1allD2
10X-RAY DIFFRACTION1allD3

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