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- PDB-5nsk: apo Structure of Leucyl aminopeptidase from Trypanosoma brucei -

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Basic information

Entry
Database: PDB / ID: 5nsk
Titleapo Structure of Leucyl aminopeptidase from Trypanosoma brucei
ComponentsAminopeptidase, putative
KeywordsHYDROLASE / M17 leucyl aminopeptidase / aminopeptidase / tryanosoma brucei
Function / homology
Function and homology information


metalloaminopeptidase activity / aminopeptidase activity / peptidase 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
Aminopeptidase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTimm, J. / Wilson, K.S.
Funding support Spain, 5items
OrganizationGrant numberCountry
European CommissionGA223238
European CommissionGA290080
RICET FIS NetworkRD12/0018/0017 Spain
Junta de AndaluciaBIO-199, P12-BIO-2059 Spain
Plan NacionalSAF2016-79957-R Spain
CitationJournal: mSphere / Year: 2018
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 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: 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 21, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Mar 28, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.4Jan 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, putative
B: Aminopeptidase, putative
C: Aminopeptidase, putative
D: Aminopeptidase, putative
E: Aminopeptidase, putative
F: Aminopeptidase, putative


Theoretical massNumber of molelcules
Total (without water)332,5096
Polymers332,5096
Non-polymers00
Water9,008500
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24940 Å2
ΔGint-62 kcal/mol
Surface area93830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.330, 162.450, 176.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULYSLYSAA5 - 5204 - 520
21LEULEULYSLYSBB5 - 5204 - 520
12LEULEULYSLYSAA5 - 5204 - 520
22LEULEULYSLYSCC5 - 5204 - 520
13LEULEULYSLYSAA5 - 5204 - 520
23LEULEULYSLYSDD5 - 5204 - 520
14LEULEULYSLYSAA5 - 5204 - 520
24LEULEULYSLYSEE5 - 5204 - 520
15THRTHRLEULEUAA4 - 5213 - 521
25THRTHRLEULEUFF4 - 5213 - 521
16LEULEULEULEUBB5 - 5214 - 521
26LEULEULEULEUCC5 - 5214 - 521
17LEULEULEULEUBB5 - 5214 - 521
27LEULEULEULEUDD5 - 5214 - 521
18LEULEULEULEUBB5 - 5214 - 521
28LEULEULEULEUEE5 - 5214 - 521
19LEULEULEULEUBB5 - 5214 - 521
29LEULEULEULEUFF5 - 5214 - 521
110LEULEULEULEUCC5 - 5214 - 521
210LEULEULEULEUDD5 - 5214 - 521
111LEULEULEULEUCC5 - 5214 - 521
211LEULEULEULEUEE5 - 5214 - 521
112LEULEULEULEUCC5 - 5214 - 521
212LEULEULEULEUFF5 - 5214 - 521
113LEULEULEULEUDD5 - 5214 - 521
213LEULEULEULEUEE5 - 5214 - 521
114LEULEULEULEUDD5 - 5214 - 521
214LEULEULEULEUFF5 - 5214 - 521
115LEULEULEULEUEE5 - 5214 - 521
215LEULEULEULEUFF5 - 5214 - 521

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Aminopeptidase, putative


Mass: 55418.141 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb11.02.4440 / Production host: Escherichia coli (E. coli) / References: UniProt: Q385B0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 500 / 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: 3.51 Å3/Da / Density % sol: 64.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.8 M Na citrate pH 7.0, 5 mM CoSO4

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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: Apr 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→72.61 Å / Num. obs: 143992 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.165 / Net I/σ(I): 9.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.019 / Mean I/σ(I) obs: 2 / Num. unique all: 7106 / % 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: 2HB6 poly-Ala model

2hb6


Resolution: 2.6→72.61 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.272 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.227 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21085 7257 5 %RANDOM
Rwork0.19113 ---
obs0.19212 136637 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.096 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å2-0 Å2
2--0.71 Å20 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2.6→72.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22152 0 0 500 22652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01922596
X-RAY DIFFRACTIONr_bond_other_d0.0080.0221166
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.96230873
X-RAY DIFFRACTIONr_angle_other_deg2.006348506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01753027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34424.252889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.692153222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.35215111
X-RAY DIFFRACTIONr_chiral_restr0.0850.23653
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02126306
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024973
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_it2.0763.84412144
X-RAY DIFFRACTIONr_mcbond_other2.0763.84412143
X-RAY DIFFRACTIONr_mcangle_it3.3775.75815159
X-RAY DIFFRACTIONr_mcangle_other3.3775.75815160
X-RAY DIFFRACTIONr_scbond_it2.2573.97810452
X-RAY DIFFRACTIONr_scbond_other2.2573.97810453
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5935.90115715
X-RAY DIFFRACTIONr_long_range_B_refined5.18130.13524740
X-RAY DIFFRACTIONr_long_range_B_other5.16930.11724601
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A586680.05
12B586680.05
21A590780.05
22C590780.05
31A591500.03
32D591500.03
41A589800.04
42E589800.04
51A591220.04
52F591220.04
61B588800.06
62C588800.06
71B589120.05
72D589120.05
81B586500.06
82E586500.06
91B584860.05
92F584860.05
101C592680.05
102D592680.05
111C595480.05
112E595480.05
121C593540.05
122F593540.05
131D592520.04
132E592520.04
141D588740.04
142F588740.04
151E592660.05
152F592660.05
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 549 -
Rwork0.309 10030 -
obs--100 %

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