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- PDB-5egy: Structure of ligand free human DPP3 in closed form. -

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Basic information

Entry
Database: PDB / ID: 5egy
TitleStructure of ligand free human DPP3 in closed form.
ComponentsDipeptidyl peptidase 3
KeywordsHYDROLASE / Unbound / Peptidase / Zinc
Function / homology
Function and homology information


dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / KEAP1-NFE2L2 pathway / Neddylation / proteolysis / extracellular exosome / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Fructose-1,6-Bisphosphatase; Chain A, domain 1 - #30 / Alpha-Beta Plaits - #2600 / Dipeptidyl-peptidase 3 / Peptidase family M49 / Peptidase family M49 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dipeptidyl peptidase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.741 Å
AuthorsKumar, P. / Reithofer, V. / Reisinger, M. / Pavkov-Keller, T. / Wallner, S. / Macheroux, P. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW901 Austria
CitationJournal: Sci Rep / Year: 2016
Title: Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition.
Authors: Kumar, P. / Reithofer, V. / Reisinger, M. / Wallner, S. / Pavkov-Keller, T. / Macheroux, P. / Gruber, K.
History
DepositionOct 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6383
Polymers81,5491
Non-polymers902
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-45 kcal/mol
Surface area27940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.190, 106.206, 62.572
Angle α, β, γ (deg.)90.00, 91.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-914-

HOH

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Components

#1: Protein Dipeptidyl peptidase 3 / Dipeptidyl aminopeptidase III / Dipeptidyl arylamidase III / Dipeptidyl peptidase III / DPP III / ...Dipeptidyl aminopeptidase III / Dipeptidyl arylamidase III / Dipeptidyl peptidase III / DPP III / Enkephalinase B


Mass: 81548.688 Da / Num. of mol.: 1 / Mutation: C19S, E207C, E451A, S491C, C519S, C654S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP3 / Plasmid: PET28MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q9NY33, dipeptidyl-peptidase III
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH- 8.2, 293K
PH range: 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.74→48.83 Å / Num. all: 20281 / Num. obs: 20281 / % possible obs: 98.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 69.01 Å2 / Rmerge(I) obs: 0.0723 / Rsym value: 0.0723 / Net I/σ(I): 12.01
Reflection shellResolution: 2.74→2.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.7944 / Mean I/σ(I) obs: 1.64 / % possible all: 96.02

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T6B

3t6b


Resolution: 2.741→43.83 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 1014 5 %Random selection
Rwork0.2067 ---
obs0.2091 20263 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.741→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5745 0 2 22 5769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035881
X-RAY DIFFRACTIONf_angle_d0.577964
X-RAY DIFFRACTIONf_dihedral_angle_d11.6632168
X-RAY DIFFRACTIONf_chiral_restr0.022859
X-RAY DIFFRACTIONf_plane_restr0.0031045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7408-2.88530.43251410.36272673X-RAY DIFFRACTION97
2.8853-3.0660.34871450.30922769X-RAY DIFFRACTION100
3.066-3.30270.34551470.2712778X-RAY DIFFRACTION100
3.3027-3.63490.29491440.22582746X-RAY DIFFRACTION99
3.6349-4.16050.2851450.2062753X-RAY DIFFRACTION99
4.1605-5.24040.221450.1762754X-RAY DIFFRACTION99
5.2404-43.83540.18661470.16472776X-RAY DIFFRACTION98

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