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- PDB-5ntf: apo Structure of Leucyl aminopeptidase from Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 5ntf
Titleapo Structure of Leucyl aminopeptidase from Trypanosoma cruzi
ComponentsAminopeptidase
KeywordsHYDROLASE / M17 leucyl aminopeptidase / aminopeptidase / tryanosoma cruzi
Function / homology
Function and homology information


metalloaminopeptidase activity / manganese ion binding / proteolysis / cytoplasm
Similarity search - Function
Zn-dependent exopeptidases / Probable aminopeptidase NPEPL1, N-terminal / M17 aminopeptidase N-terminal domain 2 / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Zn peptidases / Aminopeptidase / Rossmann fold ...Zn-dependent exopeptidases / Probable aminopeptidase NPEPL1, N-terminal / M17 aminopeptidase N-terminal domain 2 / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Zn peptidases / Aminopeptidase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTimm, J. / Wilson, K.
CitationJournal: mSphere / Year: 2017
Title: Structural Characterization of Acidic M17 Leucine Aminopeptidases from the TriTryps and Evaluation of Their Role in Nutrient Starvation inTrypanosoma brucei.
Authors: Timm, J. / Valente, M. / Garcia-Caballero, D. / Wilson, K.S. / Gonzalez-Pacanowska, D.
History
DepositionApr 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 24, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase
B: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,2956
Polymers111,9112
Non-polymers3844
Water2,504139
1
A: Aminopeptidase
B: Aminopeptidase
hetero molecules

A: Aminopeptidase
B: Aminopeptidase
hetero molecules

A: Aminopeptidase
B: Aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,88618
Polymers335,7336
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area25840 Å2
ΔGint-266 kcal/mol
Surface area94840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.419, 161.419, 205.107
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-602-

SO4

21B-761-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 10 - 521 / Label seq-ID: 9 - 520

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Aminopeptidase


Mass: 55955.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: TCDM_00653 / Production host: Escherichia coli (E. coli) / References: UniProt: V5BWE3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Citric acid pH 4.0, 1.6 M (NH4)2SO4, 1 mM MnCl2, 5 mM actinonin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→48.14 Å / Num. obs: 43976 / % possible obs: 96.2 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.181 / Net I/σ(I): 9.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.987 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4437 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NTG

5ntg


Resolution: 2.3→48.14 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.906 / SU B: 10.468 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.421 / ESU R Free: 0.265 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25906 2061 4.7 %RANDOM
Rwork0.20922 ---
obs0.21152 41496 95.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.635 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å2-0.89 Å20 Å2
2---1.78 Å20 Å2
3---5.78 Å2
Refinement stepCycle: 1 / Resolution: 2.3→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7523 0 20 139 7682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197693
X-RAY DIFFRACTIONr_bond_other_d0.0060.027197
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.96310487
X-RAY DIFFRACTIONr_angle_other_deg1.211316508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32651026
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18124.212311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.282151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8471543
X-RAY DIFFRACTIONr_chiral_restr0.0780.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218901
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021694
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6373.0324098
X-RAY DIFFRACTIONr_mcbond_other1.6363.0314097
X-RAY DIFFRACTIONr_mcangle_it2.6614.545120
X-RAY DIFFRACTIONr_mcangle_other2.6614.5425121
X-RAY DIFFRACTIONr_scbond_it1.9733.2523594
X-RAY DIFFRACTIONr_scbond_other1.9733.2493579
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2184.7835342
X-RAY DIFFRACTIONr_long_range_B_refined4.81223.9218314
X-RAY DIFFRACTIONr_long_range_B_other4.80723.9188291
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 60232 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 191 -
Rwork0.298 3167 -
obs--99.88 %

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