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

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Basic information

Entry
Database: PDB / ID: 6eed
TitleX-ray crystal structure of Pf-M1 in complex with inhibitor (6p) 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-J6A / PHOSPHATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)105,03216
Polymers103,6321
Non-polymers1,40115
Water25,7431429
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)75.149, 109.230, 117.920
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 , 7 types, 1444 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-J6A / (2R)-2-[(cyclohexylacetyl)amino]-N-hydroxy-2-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)acetamide


Mass: 420.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H23F3N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1429 / 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: 47.32 % / Mosaicity: 0.44 °
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: Feb 6, 2015
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: 1.5→44.18 Å / Num. obs: 153713 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 14.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.9 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.5-1.531.13972090.5830.4911.24595.4
8.22-44.180.03210690.9930.0150.03698.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→35.801 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.83
RfactorNum. reflection% reflection
Rfree0.1796 7585 4.94 %
Rwork0.1539 --
obs0.1552 153615 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.33 Å2 / Biso mean: 21.1039 Å2 / Biso min: 7.72 Å2
Refinement stepCycle: final / Resolution: 1.5→35.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7253 0 86 1429 8768
Biso mean--26.77 34.97 -
Num. residues----889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127661
X-RAY DIFFRACTIONf_angle_d1.35910400
X-RAY DIFFRACTIONf_chiral_restr0.0631145
X-RAY DIFFRACTIONf_plane_restr0.0071324
X-RAY DIFFRACTIONf_dihedral_angle_d13.5762922
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 (%)
1.5-1.51710.27842400.25744585482594
1.5171-1.53490.30142410.24894728496997
1.5349-1.55360.25282510.24084750500198
1.5536-1.57330.2622330.22384788502198
1.5733-1.5940.24992360.21844781501798
1.594-1.61580.24332350.19994801503699
1.6158-1.63890.22032420.19664814505698
1.6389-1.66340.25462390.19014796503599
1.6634-1.68940.21782450.18374825507099
1.6894-1.71710.2342800.18374763504398
1.7171-1.74670.2272170.18354895511299
1.7467-1.77840.20982350.17564823505899
1.7784-1.81260.20682460.16914865511199
1.8126-1.84960.19012270.16614875510299
1.8496-1.88980.19172560.16024819507599
1.8898-1.93380.18792610.16184871513299
1.9338-1.98220.20592530.15464844509799
1.9822-2.03570.17132590.14864904516399
2.0357-2.09560.16592800.14684839511999
2.0956-2.16330.1662790.144248575136100
2.1633-2.24060.17362540.142548845138100
2.2406-2.33030.17072640.144949385202100
2.3303-2.43630.18012390.14849185157100
2.4363-2.56470.17762820.150449115193100
2.5647-2.72540.17492560.150549395195100
2.7254-2.93570.18632650.150149385203100
2.9357-3.2310.16422610.139749855246100
3.231-3.69810.13422490.128150205269100
3.6981-4.65760.14272570.123350615318100
4.6576-35.81120.17113030.152152135516100
Refinement TLS params.Method: refined / Origin x: 17.9727 Å / Origin y: 3.8579 Å / Origin z: 10.3056 Å
111213212223313233
T0.0774 Å2-0.0065 Å20.009 Å2-0.0917 Å20.0089 Å2--0.0837 Å2
L0.3217 °2-0.1373 °20.0276 °2-0.6049 °20.1104 °2--0.5041 °2
S-0.0311 Å °-0.0069 Å °0.0283 Å °-0.013 Å °0.0063 Å °-0.0073 Å °-0.0366 Å °-0.0002 Å °0.0245 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA196 - 1084
2X-RAY DIFFRACTION1allB1001 - 2001
3X-RAY DIFFRACTION1allS1 - 1473
4X-RAY DIFFRACTION1allC1 - 4001

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