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- PDB-6ee4: X-ray crystal structure of Pf-M1 in complex with inhibitor (6m) a... -

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Basic information

Entry
Database: PDB / ID: 6ee4
TitleX-ray crystal structure of Pf-M1 in complex with inhibitor (6m) 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 / 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-J4S / PHOSPHATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 13, 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)104,94216
Polymers103,6321
Non-polymers1,31115
Water27,0041499
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)75.110, 108.860, 118.080
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 196 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 , 6 types, 1514 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-J4S / (2R)-2-[(cyclopropylacetyl)amino]-N-hydroxy-2-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)acetamide


Mass: 378.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17F3N2O3 / 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1499 / 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: 2.33 Å3/Da / Density % sol: 47.19 % / Mosaicity: 0.42 °
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 15, 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: 1.58→46.42 Å / Num. obs: 133245 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 13.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.063 / Rrim(I) all: 0.169 / Net I/σ(I): 9.3 / Num. measured all: 964069 / Scaling rejects: 41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.58-1.66.51.44563960.470.6011.56898.2
8.64-46.4260.0639270.9950.0270.06898.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.9data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→41.291 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.23
RfactorNum. reflection% reflection
Rfree0.1887 6534 4.91 %
Rwork0.1578 --
obs0.1594 133146 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.68 Å2 / Biso mean: 19.8572 Å2 / Biso min: 6.2 Å2
Refinement stepCycle: final / Resolution: 1.58→41.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7266 0 78 1499 8843
Biso mean--28.6 34.63 -
Num. residues----889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067726
X-RAY DIFFRACTIONf_angle_d0.8110500
X-RAY DIFFRACTIONf_chiral_restr0.0521151
X-RAY DIFFRACTIONf_plane_restr0.0051342
X-RAY DIFFRACTIONf_dihedral_angle_d4.7166494
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 (%)
1.578-1.59590.28361840.26994131431597
1.5959-1.61470.27981990.247341434342100
1.6147-1.63440.28382090.242441794388100
1.6344-1.65510.28282190.244841874406100
1.6551-1.67690.25142060.241341884394100
1.6769-1.69980.27682240.232141574381100
1.6998-1.72410.27732200.226941694389100
1.7241-1.74990.25731960.232742214417100
1.7499-1.77720.2362230.212541694392100
1.7772-1.80630.2692340.204541924426100
1.8063-1.83750.22612350.193641704405100
1.8375-1.87090.21481880.183342334421100
1.8709-1.90690.20542030.176842054408100
1.9069-1.94580.22172340.172741934427100
1.9458-1.98810.20522200.165441624382100
1.9881-2.03440.22250.164642394464100
2.0344-2.08520.17972160.158742044420100
2.0852-2.14160.20112250.147941794404100
2.1416-2.20460.17622100.14242204430100
2.2046-2.27580.16562200.142642474467100
2.2758-2.35710.18352210.149841984419100
2.3571-2.45150.19182330.149742114444100
2.4515-2.5630.1862380.148541964434100
2.563-2.69820.19372350.148642324467100
2.6982-2.86720.17551940.143542994493100
2.8672-3.08850.16992310.138542304461100
3.0885-3.39910.15982060.12943074513100
3.3991-3.89070.13962110.119343104521100
3.8907-4.90060.14692380.117743414579100
4.9006-41.30550.16462370.158445004737100
Refinement TLS params.Method: refined / Origin x: -17.7891 Å / Origin y: 4.2104 Å / Origin z: -10.513 Å
111213212223313233
T0.0674 Å20.0057 Å20.0047 Å2-0.0864 Å2-0.0094 Å2--0.0699 Å2
L0.2791 °20.1086 °2-0.024 °2-0.5965 °2-0.1028 °2--0.4139 °2
S-0.0267 Å °0.0019 Å °0.0226 Å °0.0005 Å °0.0026 Å °0.0142 Å °-0.0169 Å °-0.0044 Å °0.025 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA196 - 1084
2X-RAY DIFFRACTION1allB1 - 1001
3X-RAY DIFFRACTION1allC1 - 6
4X-RAY DIFFRACTION1allS1 - 1572
5X-RAY DIFFRACTION1allD1 - 3
6X-RAY DIFFRACTION1allE1 - 6

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