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- PDB-3t6j: Structure of human DPPIII in complex with the opioid peptide Tyno... -

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Basic information

Entry
Database: PDB / ID: 3t6j
TitleStructure of human DPPIII in complex with the opioid peptide Tynorphin, at 3.0 Angstroms
Components
  • Dipeptidyl peptidase 3
  • Tynorphin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / human dipeptidylpeptidase III / entropy binding / opioid peptide complex / domain motion / HYDROLASE-HYDROLASE INHIBITOR complex
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 / molecular replacement / Resolution: 2.976 Å
AuthorsBezerra, G.A. / Gruber, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III.
Authors: Bezerra, G.A. / Dobrovetsky, E. / Viertlmayr, R. / Dong, A. / Binter, A. / Abramic, M. / Macheroux, P. / Dhe-Paganon, S. / Gruber, K.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Mar 13, 2013Group: Other
Revision 1.4Jun 19, 2013Group: Database references
Revision 1.5Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptidyl peptidase 3
B: Tynorphin


Theoretical massNumber of molelcules
Total (without water)82,2702
Polymers82,2702
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-10 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.013, 107.274, 65.478
Angle α, β, γ (deg.)90.00, 93.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 81606.789 Da / Num. of mol.: 1 / Mutation: E451A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP3, hDPPIII / Plasmid: pET28MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NY33, dipeptidyl-peptidase III
#2: Protein/peptide Tynorphin


Mass: 662.775 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: truncated version of a human opioid peptide, Spinorphin
Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Compound detailssynthetic opioid peptide

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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: 2.53 Å3/Da / Density % sol: 51.29 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.2
Details: 0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH 8.2, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 31, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionRedundancy: 2.4 % / Av σ(I) over netI: 4.8 / Number: 39160 / Rsym value: 0.06 / D res high: 2.973 Å / D res low: 79.907 Å / Num. obs: 16399 / % possible obs: 96.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
9.419.984.110.0110.0112.4
6.659.496.210.020.022.5
5.436.6597.410.0370.0372.5
4.75.4397.410.0340.0342.4
4.24.797.810.0370.0372.4
3.844.297.910.0660.0662.4
3.553.8498.410.1170.1172.4
3.323.5598.310.1160.1162.4
3.133.3298.310.150.152.4
2.973.1392.410.2450.2452.2
ReflectionResolution: 2.973→79.907 Å / Num. all: 16399 / Num. obs: 16399 / % possible obs: 96.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.4 % / Rsym value: 0.06 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.973-3.132.20.3150.2453505622990.1950.3150.245392.4
3.13-3.322.40.1910.155.1550822980.1170.1910.154.598.3
3.32-3.552.40.1510.1163521721650.0950.1510.1166.198.3
3.55-3.842.40.1520.1172.8488820360.0950.1520.1176.498.4
3.84-4.22.40.0870.0662.3445218450.0550.0870.0669.397.9
4.2-4.72.40.0470.03721.1403116680.0290.0470.0371197.8
4.7-5.432.40.0430.03422.7354814560.0270.0430.03411.597.4
5.43-6.652.50.0470.03714.5305712470.0290.0470.03711.997.4
6.65-9.42.50.0260.0233.323189390.0160.0260.0215.296.2
9.4-19.9012.40.0150.01154.910854460.0090.0150.01118.984.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.98 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.97 Å19.9 Å
Translation2.97 Å19.9 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
DNAdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FVY

3fvy


Resolution: 2.976→19.6 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7967 / SU ML: 0.34 / σ(F): 1.33 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 828 5.07 %
Rwork0.2366 --
all0.2382 16399 -
obs0.2382 16343 96.12 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.914 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso max: 259.39 Å2 / Biso mean: 68.9701 Å2 / Biso min: 7.89 Å2
Baniso -1Baniso -2Baniso -3
1-2.4562 Å2-0 Å20.1545 Å2
2---2.3001 Å2-0 Å2
3----0.1561 Å2
Refinement stepCycle: LAST / Resolution: 2.976→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 0 7 5787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076133
X-RAY DIFFRACTIONf_angle_d0.8468015
X-RAY DIFFRACTIONf_chiral_restr0.062863
X-RAY DIFFRACTIONf_plane_restr0.0031050
X-RAY DIFFRACTIONf_dihedral_angle_d15.1722178
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9756-3.16130.32871380.31022521265994
3.1613-3.40420.32431360.28872613274998
3.4042-3.74460.32421090.30442626273597
3.7446-4.28150.29831410.2372617275897
4.2815-5.37580.25251540.19582600275497
5.3758-19.60040.20241500.18562538268894

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