[English] 日本語
Yorodumi
- PDB-5nsq: Structure of Leucyl aminopeptidase from Trypanosoma brucei in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nsq
TitleStructure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Actinonin
ComponentsAminopeptidase, putative
KeywordsHYDROLASE / M17 leucyl aminopeptidase / aminopeptidase / tryanosoma brucei actinonin
Function / homology
Function and homology information


metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / peptidase activity / 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
ACTINONIN / : / Aminopeptidase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTimm, J. / Wilson, K.
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 ...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 / 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 / _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_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminopeptidase, putative
B: Aminopeptidase, putative
C: Aminopeptidase, putative
D: Aminopeptidase, putative
E: Aminopeptidase, putative
F: Aminopeptidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,56524
Polymers332,5936
Non-polymers2,97218
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33720 Å2
ΔGint-166 kcal/mol
Surface area91320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.909, 165.730, 121.980
Angle α, β, γ (deg.)90.00, 112.45, 90.00
Int Tables number4
Space group name H-MP1211
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: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUAA3 - 5213 - 521
21THRTHRLEULEUBB3 - 5213 - 521
12LEULEULYSLYSAA4 - 5204 - 520
22LEULEULYSLYSCC4 - 5204 - 520
13THRTHRLEULEUAA3 - 5213 - 521
23THRTHRLEULEUDD3 - 5213 - 521
14THRTHRLEULEUAA3 - 5213 - 521
24THRTHRLEULEUEE3 - 5213 - 521
15THRTHRLEULEUAA3 - 5213 - 521
25THRTHRLEULEUFF3 - 5213 - 521
16LEULEULYSLYSBB4 - 5204 - 520
26LEULEULYSLYSCC4 - 5204 - 520
17THRTHRLEULEUBB3 - 5213 - 521
27THRTHRLEULEUDD3 - 5213 - 521
18THRTHRLEULEUBB3 - 5213 - 521
28THRTHRLEULEUEE3 - 5213 - 521
19THRTHRLEULEUBB3 - 5213 - 521
29THRTHRLEULEUFF3 - 5213 - 521
110LEULEULYSLYSCC4 - 5204 - 520
210LEULEULYSLYSDD4 - 5204 - 520
111LEULEULYSLYSCC4 - 5204 - 520
211LEULEULYSLYSEE4 - 5204 - 520
112LEULEULEULEUCC4 - 5214 - 521
212LEULEULEULEUFF4 - 5214 - 521
113THRTHRLEULEUDD3 - 5213 - 521
213THRTHRLEULEUEE3 - 5213 - 521
114THRTHRLEULEUDD3 - 5213 - 521
214THRTHRLEULEUFF3 - 5213 - 521
115THRTHRLEULEUEE3 - 5213 - 521
215THRTHRLEULEUFF3 - 5213 - 521

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

-
Components

#1: Protein
Aminopeptidase, putative / / leucyl aminopeptidase


Mass: 55432.168 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: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-BB2 / ACTINONIN / 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE / Actinonin


Mass: 385.498 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H35N3O5 / Comment: antitumor, antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.0, 2.4 M (NH4)2SO4, 5 mM MnSO4, 5 mM actinonin

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→41.5 Å / Num. obs: 68219 / % possible obs: 97 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 4.5
Reflection shellResolution: 3→3.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / Num. unique all: 4424 / % possible all: 98

-
Processing

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

5nsk


Resolution: 3→41.5 Å / Cor.coef. Fo:Fc: 0.823 / Cor.coef. Fo:Fc free: 0.784 / SU B: 27.827 / SU ML: 0.47 / Cross valid method: THROUGHOUT / ESU R Free: 0.547 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29641 3327 4.9 %RANDOM
Rwork0.26464 ---
obs0.26617 63948 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.895 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0 Å20.22 Å2
2---3.67 Å2-0 Å2
3---1.8 Å2
Refinement stepCycle: 1 / Resolution: 3→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22467 0 174 34 22675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01923204
X-RAY DIFFRACTIONr_bond_other_d0.0060.0221588
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.97231632
X-RAY DIFFRACTIONr_angle_other_deg1.254349500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03953113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43924.314874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.316153224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.98615100
X-RAY DIFFRACTIONr_chiral_restr0.0720.23745
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02126944
X-RAY DIFFRACTIONr_gen_planes_other0.0050.025032
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_it2.7733.69912446
X-RAY DIFFRACTIONr_mcbond_other2.7723.69912445
X-RAY DIFFRACTIONr_mcangle_it4.5935.54315549
X-RAY DIFFRACTIONr_mcangle_other4.5935.54415550
X-RAY DIFFRACTIONr_scbond_it2.0873.70610758
X-RAY DIFFRACTIONr_scbond_other2.0873.70610759
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6325.55916080
X-RAY DIFFRACTIONr_long_range_B_refined6.1628.67923979
X-RAY DIFFRACTIONr_long_range_B_other6.1628.6823980
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)
11A586300.06
12B586300.06
21A591440.05
22C591440.05
31A579860.05
32D579860.05
41A585220.05
42E585220.05
51A558200.05
52F558200.05
61B592080.05
62C592080.05
71B581800.05
72D581800.05
81B591960.05
82E591960.05
91B551880.06
92F551880.06
101C581700.05
102D581700.05
111C589080.05
112E589080.05
121C556600.05
122F556600.05
131D582920.05
132E582920.05
141D549580.05
142F549580.05
151E553360.06
152F553360.06
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 272 -
Rwork0.35 4810 -
obs--97.69 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more