[English] 日本語
Yorodumi
- PDB-5na8: Structure of DPP III from Bacteroides thetaiotaomicron in closed form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5na8
TitleStructure of DPP III from Bacteroides thetaiotaomicron in closed form
ComponentsPutative dipeptidyl-peptidase III
KeywordsHYDROLASE / Bacteroides thetaiotaomicron / Metallopeptidase / Dipeptidyl peptidase III / Zinc-Hydrolase / closed form
Function / homologyPeptidase family M49 / Peptidase family M49 / hydrolase activity / metal ion binding / Dipeptidyl-peptidase III
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.29 Å
AuthorsSabljic, I. / Luic, M.
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structure of dipeptidyl peptidase III from the human gut symbiont Bacteroides thetaiotaomicron.
Authors: Sabljic, I. / Mestrovic, N. / Vukelic, B. / Macheroux, P. / Gruber, K. / Luic, M. / Abramic, M.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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: Putative dipeptidyl-peptidase III
B: Putative dipeptidyl-peptidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8908
Polymers155,3752
Non-polymers5156
Water0
1
A: Putative dipeptidyl-peptidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8493
Polymers77,6881
Non-polymers1612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative dipeptidyl-peptidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0415
Polymers77,6881
Non-polymers3544
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.632, 176.315, 74.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 25 and (name N or name...
21(chain B and (resseq 25 or (resid 26 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASP(chain A and ((resid 25 and (name N or name...AA2525
12ASPASPASNASN(chain A and ((resid 25 and (name N or name...AA25 - 67525 - 675
13ASPASPASNASN(chain A and ((resid 25 and (name N or name...AA25 - 67525 - 675
14ASPASPASNASN(chain A and ((resid 25 and (name N or name...AA25 - 67525 - 675
15ASPASPASNASN(chain A and ((resid 25 and (name N or name...AA25 - 67525 - 675
21ASPASPASPASP(chain B and (resseq 25 or (resid 26 and (name...BB2525
22TYRTYRTYRTYR(chain B and (resseq 25 or (resid 26 and (name...BB2626
23PHEPHEASNASN(chain B and (resseq 25 or (resid 26 and (name...BB24 - 67424 - 674
24PHEPHEASNASN(chain B and (resseq 25 or (resid 26 and (name...BB24 - 67424 - 674
25PHEPHEASNASN(chain B and (resseq 25 or (resid 26 and (name...BB24 - 67424 - 674
26PHEPHEASNASN(chain B and (resseq 25 or (resid 26 and (name...BB24 - 67424 - 674
27PHEPHEASNASN(chain B and (resseq 25 or (resid 26 and (name...BB24 - 67424 - 674
28PHEPHEASNASN(chain B and (resseq 25 or (resid 26 and (name...BB24 - 67424 - 674
29PHEPHEASNASN(chain B and (resseq 25 or (resid 26 and (name...BB24 - 67424 - 674

-
Components

#1: Protein Putative dipeptidyl-peptidase III /


Mass: 77687.539 Da / Num. of mol.: 2 / Mutation: C11S, C158S, C189S, C425S, C450S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_1846 / Plasmid: pET-21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A6N1, dipeptidyl-peptidase III
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M NaCl, 0.1 M sodium cocodylate pH 6.5, 2.0 M NH4SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 12, 2015
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.27→47.49 Å / Num. obs: 25217 / % possible obs: 97.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 47.3 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.229 / Rpim(I) all: 0.109 / Rrim(I) all: 0.254 / Net I/σ(I): 7.8 / Num. measured all: 134890 / Scaling rejects: 35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.27-3.494.50.5920.8310.3050.66987.1
9.24-47.495.40.0760.9950.0350.08499.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.329
Highest resolutionLowest resolution
Rotation47.49 Å3.4 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.17data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NA6

5na6


Resolution: 3.29→47.488 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.16
RfactorNum. reflection% reflection
Rfree0.2506 1241 4.94 %
Rwork0.2072 --
obs0.2093 25121 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.14 Å2 / Biso mean: 41.0014 Å2 / Biso min: 12.85 Å2
Refinement stepCycle: final / Resolution: 3.29→47.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10198 0 22 0 10220
Biso mean--51.15 --
Num. residues----1300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210443
X-RAY DIFFRACTIONf_angle_d0.41614189
X-RAY DIFFRACTIONf_chiral_restr0.0391556
X-RAY DIFFRACTIONf_plane_restr0.0031849
X-RAY DIFFRACTIONf_dihedral_angle_d11.3866162
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5581X-RAY DIFFRACTION6.792TORSIONAL
12B5581X-RAY DIFFRACTION6.792TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2896-3.42120.33621330.27622474260794
3.4212-3.57690.33151540.252325932747100
3.5769-3.76540.29361400.22126412781100
3.7654-4.00120.22611250.195126432768100
4.0012-4.310.23981310.191926502781100
4.31-4.74330.22281170.18922673279099
4.7433-5.42890.23781370.1882672280999
5.4289-6.83650.24011330.228927182851100
6.8365-47.49270.20881710.183228162987100

+
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