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- PDB-6ee3: X-ray crystal structure of Pf-M1 in complex with inhibitor (6k) a... -

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Basic information

Entry
Database: PDB / ID: 6ee3
TitleX-ray crystal structure of Pf-M1 in complex with inhibitor (6k) 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-J4V / PHOSPHATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.82 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)104,53210
Polymers103,6321
Non-polymers9009
Water23,0411279
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)74.960, 108.601, 118.160
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, 1288 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-J4V / (1R,2r,3S,5R,7R)-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]tricyclo[3.3.1.1~3,7~]decane-2-carboxamide


Mass: 458.473 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H25F3N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1279 / 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: 2.32 Å3/Da / Density % sol: 46.99 % / Mosaicity: 0.34 °
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: 1.82→54.3 Å / Num. obs: 87047 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 13.76 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.072 / Rrim(I) all: 0.196 / Net I/σ(I): 8.9 / Num. measured all: 637254 / Scaling rejects: 611
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.82-1.856.90.99643630.640.4061.07799.3
9.8-54.35.80.0576520.9930.0260.06398.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimless0.5.9data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementResolution: 1.82→46.401 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.76
RfactorNum. reflection% reflection
Rfree0.1957 4390 5.05 %
Rwork0.1511 --
obs0.1533 86961 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.2 Å2 / Biso mean: 16.9036 Å2 / Biso min: 5.37 Å2
Refinement stepCycle: final / Resolution: 1.82→46.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7239 0 55 1279 8573
Biso mean--25.01 29.68 -
Num. residues----889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017533
X-RAY DIFFRACTIONf_angle_d1.20810224
X-RAY DIFFRACTIONf_chiral_restr0.111130
X-RAY DIFFRACTIONf_plane_restr0.0061306
X-RAY DIFFRACTIONf_dihedral_angle_d12.9872866
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 (%)
1.82-1.84070.28081270.23322694282199
1.8407-1.86230.31721380.218227182856100
1.8623-1.88510.26131530.215127222875100
1.8851-1.90890.22321380.199327392877100
1.9089-1.9340.27421460.200426862832100
1.934-1.96050.22271540.187327192873100
1.9605-1.98850.23351310.17827352866100
1.9885-2.01820.20331380.176727262864100
2.0182-2.04980.21281660.171227232889100
2.0498-2.08340.23311460.163527632909100
2.0834-2.11930.20151640.155626642828100
2.1193-2.15780.20231460.152927292875100
2.1578-2.19930.20641650.147827352900100
2.1993-2.24420.21021160.150427402856100
2.2442-2.2930.19451500.153927372887100
2.293-2.34630.21741430.154227382881100
2.3463-2.4050.19211420.152327522894100
2.405-2.470.23621330.150327602893100
2.47-2.54270.20811640.149927112875100
2.5427-2.62480.20081410.150327512892100
2.6248-2.71860.20341530.153827582911100
2.7186-2.82740.20751450.154927332878100
2.8274-2.95610.21231510.14727802931100
2.9561-3.11190.20191450.144527782923100
3.1119-3.30680.1861390.13627742913100
3.3068-3.56210.15241280.125128102938100
3.5621-3.92040.14591520.119927922944100
3.9204-4.48720.16441450.11728042949100
4.4872-5.65190.14361540.126728503004100
5.6519-46.41570.17641770.168329503127100
Refinement TLS params.Method: refined / Origin x: 92.7083 Å / Origin y: 112.8746 Å / Origin z: 10.5153 Å
111213212223313233
T0.0609 Å2-0.0077 Å20.0026 Å2-0.0791 Å20.0076 Å2--0.0595 Å2
L0.2466 °2-0.0813 °2-0.0404 °2-0.5331 °20.0938 °2--0.3385 °2
S-0.0247 Å °0.004 Å °0.0081 Å °-0.0052 Å °0.0021 Å °-0.0122 Å °-0.0054 Å °0.0104 Å °0.0233 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA196 - 1084
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allC1 - 7
4X-RAY DIFFRACTION1allS1 - 1324

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