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- PDB-4zx5: X-ray crystal structure of PfA-M1 in complex with hydroxamic acid... -

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Basic information

Entry
Database: PDB / ID: 4zx5
TitleX-ray crystal structure of PfA-M1 in complex with hydroxamic acid-based inhibitor 10q
ComponentsM1 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / M1 ALANYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / 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 / chloroplast / proteolysis / zinc ion binding ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / chloroplast / 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 / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / 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-4TM / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDrinkwater, N. / McGowan, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1063786 Australia
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions.
Authors: Drinkwater, N. / Vinh, N.B. / Mistry, S.N. / Bamert, R.S. / Ruggeri, C. / Holleran, J.P. / Loganathan, S. / Paiardini, A. / Charman, S.A. / Powell, A.K. / Avery, V.M. / McGowan, S. / Scammells, P.J.
History
DepositionMay 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
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)104,4568
Polymers103,7611
Non-polymers6957
Water17,655980
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.810, 109.030, 117.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 103760.719 Da / Num. of mol.: 1 / Fragment: UNP residues 195-1084 / Mutation: N213Q, N223Q, H378P, N501Q, N795Q, N1069Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate FcB1 / Columbia / Plasmid: PTRCHIS-2B / 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, 987 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 332.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N2O3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 980 / 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: 2.31 Å3/Da / Density % sol: 46.87 %
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 26, 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: 1.95→31.56 Å / Num. obs: 70857 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.31 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 11.1
Reflection shellResolution: 1.95→1.99 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.276 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Blu-Icedata collection
MOSFLMdata reduction
PHASERphasing
Aimlessdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EBG

3ebg


Resolution: 1.95→31.56 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 3579 5.06 %
Rwork0.165 --
obs0.167 70775 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.46 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7240 0 40 980 8260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077526
X-RAY DIFFRACTIONf_angle_d1.01610211
X-RAY DIFFRACTIONf_dihedral_angle_d13.1622843
X-RAY DIFFRACTIONf_chiral_restr0.0411128
X-RAY DIFFRACTIONf_plane_restr0.0051307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97570.32721210.2632569X-RAY DIFFRACTION100
1.9757-2.00270.32031270.25752543X-RAY DIFFRACTION100
2.0027-2.03140.29691410.23552578X-RAY DIFFRACTION100
2.0314-2.06170.25521500.2242519X-RAY DIFFRACTION100
2.0617-2.09390.23681480.212543X-RAY DIFFRACTION100
2.0939-2.12820.22651470.19772557X-RAY DIFFRACTION100
2.1282-2.16490.23751440.19692532X-RAY DIFFRACTION100
2.1649-2.20420.26971360.1942575X-RAY DIFFRACTION100
2.2042-2.24660.23151200.18642543X-RAY DIFFRACTION100
2.2466-2.29250.22021360.18942581X-RAY DIFFRACTION100
2.2925-2.34230.26861310.18342547X-RAY DIFFRACTION100
2.3423-2.39680.22691350.18542589X-RAY DIFFRACTION100
2.3968-2.45670.25291190.17812564X-RAY DIFFRACTION100
2.4567-2.52310.23461550.16962559X-RAY DIFFRACTION100
2.5231-2.59730.21331390.17282572X-RAY DIFFRACTION100
2.5973-2.68110.23171330.17612609X-RAY DIFFRACTION100
2.6811-2.77690.24151430.17262548X-RAY DIFFRACTION100
2.7769-2.8880.24411370.17042579X-RAY DIFFRACTION100
2.888-3.01930.22281420.15742581X-RAY DIFFRACTION100
3.0193-3.17830.19981310.15772595X-RAY DIFFRACTION100
3.1783-3.37730.18651310.14992606X-RAY DIFFRACTION100
3.3773-3.63770.16971290.13632607X-RAY DIFFRACTION100
3.6377-4.00310.15711440.13282625X-RAY DIFFRACTION100
4.0031-4.58090.15841260.12412654X-RAY DIFFRACTION100
4.5809-5.76560.15521470.13092669X-RAY DIFFRACTION100
5.7656-31.56830.1751670.16232752X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 92.3071 Å / Origin y: 113.0077 Å / Origin z: 10.2482 Å
111213212223313233
T0.101 Å20.0004 Å20.0087 Å2-0.13 Å20.0192 Å2--0.1035 Å2
L0.4766 °2-0.1579 °2-0.0131 °2-1.0434 °20.3245 °2--0.7776 °2
S-0.0724 Å °-0.0287 Å °0.0417 Å °0.0246 Å °0.0116 Å °0.0078 Å °-0.048 Å °-0.0044 Å °0.0529 Å °
Refinement TLS groupSelection details: ALL

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