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- PDB-5y1s: Crystal structure of Plasmodium falciparum aminopeptidase N in co... -

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Basic information

Entry
Database: PDB / ID: 5y1s
TitleCrystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(3,4-dimethylbenzyl)ureido)-N-hydroxy-4-methylpentanamide
ComponentsM1 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / M1-xclass Aminopeptidse / 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 / 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-E8F / Chem-E8R / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å
AuthorsMarapaka, A.K. / Zhang, Y. / Addlagatta, A.
CitationJournal: To Be Published
Title: Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(3,4-dimethylbenzyl)ureido)-N-hydroxy-4-methylpentanamide
Authors: Marapaka, A.K. / Addlagatta, A.
History
DepositionJul 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / refine_hist / struct_conn / struct_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.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)107,41311
Polymers106,2911
Non-polymers1,12110
Water10,413578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-25 kcal/mol
Surface area34890 Å2
Unit cell
Length a, b, c (Å)74.699, 109.405, 112.991
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: 106291.477 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 195-1085
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate FcB1 / Columbia / Production host: Escherichia coli (E. coli)
References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Non-polymers , 6 types, 588 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-E8F / (2S)-2-[(3,4-dimethylphenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide


Mass: 307.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N3O3
#5: Chemical ChemComp-E8R / (2R)-2-[(3,4-dimethylphenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide


Mass: 307.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N3O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsE8F and E8R are in alternate conformations of each other.

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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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, pH 8.5, 0.2M Magnesium chloride, 24% PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.66→20 Å / Num. obs: 103824 / % possible obs: 94.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.035 / Rrim(I) all: 0.085 / Χ2: 1.045 / Net I/σ(I): 19.5 / Num. measured all: 649321
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.66-1.726.50.272100760.9660.1130.2951.02193.3
1.72-1.796.50.208101670.9790.0870.2261.05393.7
1.79-1.876.50.16102180.9860.0670.1741.05694.3
1.87-1.976.50.122103090.9910.0510.1331.06495.1
1.97-2.096.40.097104480.9940.0410.1051.01595.9
2.09-2.256.50.081104820.9950.0340.0881.05696.4
2.25-2.486.40.074106050.9960.0310.081.01797.1
2.48-2.846.40.068107400.9960.0290.0741.04497.8
2.84-3.575.90.069107040.9940.0310.0761.05196.5
3.57-2050.075100750.990.0370.0841.08988.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.392
Highest resolutionLowest resolution
Rotation19.68 Å1.95 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0135refinement
DENZO2.3.1data collection
SCALEPACK2.2.0data scaling
MOLREP11.4.05model building
PDB_EXTRACT3.22data extraction
DENZO2.3.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X2U

4x2u


Resolution: 1.66→19.683 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2162 / WRfactor Rwork: 0.172 / FOM work R set: 0.884 / SU B: 1.606 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0986 / SU Rfree: 0.0971 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 5088 4.9 %RANDOM
Rwork0.1665 ---
obs0.1683 98661 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.42 Å2 / Biso mean: 27.512 Å2 / Biso min: 12.03 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.66→19.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 72 578 7958
Biso mean--31.66 32.73 -
Num. residues----890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0197607
X-RAY DIFFRACTIONr_bond_other_d0.0020.027214
X-RAY DIFFRACTIONr_angle_refined_deg2.0771.97110294
X-RAY DIFFRACTIONr_angle_other_deg1.1363.00516659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38725.04379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.008151387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2811530
X-RAY DIFFRACTIONr_chiral_restr0.1280.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028548
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021764
LS refinement shellResolution: 1.661→1.704 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 344 -
Rwork0.183 7052 -
all-7396 -
obs--92.7 %

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