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- PDB-5ntg: Structure of Leucyl aminopeptidase from Trypanosoma cruzi in comp... -

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Basic information

Entry
Database: PDB / ID: 5ntg
TitleStructure of Leucyl aminopeptidase from Trypanosoma cruzi in complex with citrate
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
CITRIC ACID / : / Aminopeptidase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 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 1.2Jan 17, 2024Group: 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 / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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)112,7899
Polymers111,9112
Non-polymers8787
Water6,882382
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)338,36827
Polymers335,7336
Non-polymers2,63521
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area31060 Å2
ΔGint-225 kcal/mol
Surface area93680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.120, 160.120, 203.672
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
11B-803-

HOH

21B-841-

HOH

31B-856-

HOH

41B-885-

HOH

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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 11 - 519 / Label seq-ID: 10 - 518

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

NCS ensembles :
ID
1
2

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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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Phosphate-citrate pH 4.2, 40 % (v/v) PEG 300, 5 mM MnSO4, 5 mM amastatin

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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: 2.32→57.31 Å / Num. obs: 43546 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.188 / Net I/σ(I): 11
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.202 / Num. unique obs: 4249 / % 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: 5NSK

5nsk


Resolution: 2.32→57.31 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.257 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20997 2183 5 %RANDOM
Rwork0.16552 ---
obs0.16772 41361 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å2-0.86 Å2-0 Å2
2---1.73 Å2-0 Å2
3---5.61 Å2
Refinement stepCycle: 1 / Resolution: 2.32→57.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7610 0 51 382 8043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197848
X-RAY DIFFRACTIONr_bond_other_d0.0060.027401
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.96810667
X-RAY DIFFRACTIONr_angle_other_deg1.258317005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52751032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26624.006327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.892151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0111551
X-RAY DIFFRACTIONr_chiral_restr0.1090.21250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219025
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021730
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_it1.7412.9934098
X-RAY DIFFRACTIONr_mcbond_other1.742.9924097
X-RAY DIFFRACTIONr_mcangle_it2.7684.4845122
X-RAY DIFFRACTIONr_mcangle_other2.7674.4855123
X-RAY DIFFRACTIONr_scbond_it2.5513.3163749
X-RAY DIFFRACTIONr_scbond_other2.5353.3123737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0364.8465527
X-RAY DIFFRACTIONr_long_range_B_refined5.6624.2348818
X-RAY DIFFRACTIONr_long_range_B_other5.66124.2358818
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 60494 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 164 -
Rwork0.282 3030 -
obs--99.97 %

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