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- PDB-5na8: Structure of DPP III from Bacteroides thetaiotaomicron in closed form -

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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
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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

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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


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

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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: 2.62 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

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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

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Phasing

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

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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

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