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- PDB-3t6b: Structure of human DPPIII in complex with the opioid peptide Tyno... -

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Basic information

Entry
Database: PDB / ID: 3t6b
TitleStructure of human DPPIII in complex with the opioid peptide Tynorphin, at 2.4 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: 2.4 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 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 3
C: Tynorphin
B: Dipeptidyl peptidase 3
D: Tynorphin


Theoretical massNumber of molelcules
Total (without water)164,5394
Polymers164,5394
Non-polymers00
Water5,098283
1
A: Dipeptidyl peptidase 3
C: Tynorphin


Theoretical massNumber of molelcules
Total (without water)82,2702
Polymers82,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-7 kcal/mol
Surface area27080 Å2
MethodPISA
2
B: Dipeptidyl peptidase 3
D: Tynorphin


Theoretical massNumber of molelcules
Total (without water)82,2702
Polymers82,2702
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-9 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.970, 107.550, 119.100
Angle α, β, γ (deg.)90.00, 90.67, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2 / 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.: 2 / 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.: 283 / 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: 2.38 Å3/Da / Density % sol: 48.38 % / Mosaicity: 0.5 °
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: ESRF / Beamline: ID14-4 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2011
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionRedundancy: 2.5 % / Av σ(I) over netI: 4.5 / Number: 139375 / Rsym value: 0.125 / D res high: 2.4 Å / D res low: 119.092 Å / Num. obs: 55412 / % possible obs: 91.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
7.5954.7183.710.0610.0612.7
5.377.5987.910.0770.0772.7
4.385.378510.0820.0822.5
3.794.3888.710.090.092.5
3.393.799010.1050.1052.5
3.13.3991.510.1330.1332.5
2.873.192.810.1810.1812.5
2.682.8793.210.2430.2432.5
2.532.6893.710.3030.3032.5
2.42.5394.110.3910.3912.5
ReflectionResolution: 2.4→119.092 Å / Num. all: 55412 / Num. obs: 55412 / % possible obs: 91.2 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Redundancy: 2.5 % / Rsym value: 0.125 / Net I/σ(I): 5.7
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
2.4-2.532.50.4950.3911.62065683170.30.4950.3912.894.1
2.53-2.682.50.3830.3031.81956978760.2310.3830.3033.493.7
2.68-2.872.50.3050.2432.61830973270.1820.3050.243493.2
2.87-3.12.50.2270.1813.61713768470.1350.2270.1814.992.8
3.1-3.392.50.1650.1334.81542861280.0970.1650.1336.291.5
3.39-3.792.50.130.1055.91394454980.0750.130.1057.790
3.79-4.382.50.1110.096.41212947950.0640.1110.098.888.7
4.38-5.372.50.1010.0827.1951538810.0590.1010.0829.285
5.37-7.592.70.0930.0777.1826630960.0530.0930.077987.9
7.59-54.7092.70.0760.0618.4442216470.0430.0760.0619.783.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.82 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å54.71 Å
Translation2.5 Å54.71 Å

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Processing

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

3fvy


Resolution: 2.4→54.709 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7997 / SU ML: 0.31 / σ(F): 0 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 4830 5.11 %RANDOM
Rwork0.1967 ---
all0.1999 ---
obs0.1999 55381 78.61 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.063 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 111.3 Å2 / Biso mean: 35.6027 Å2 / Biso min: 4.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.6274 Å2-0 Å22.6509 Å2
2---7.3677 Å2-0 Å2
3---5.7403 Å2
Refinement stepCycle: LAST / Resolution: 2.4→54.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11592 0 0 283 11875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411862
X-RAY DIFFRACTIONf_angle_d0.86916080
X-RAY DIFFRACTIONf_chiral_restr0.0691732
X-RAY DIFFRACTIONf_plane_restr0.0042108
X-RAY DIFFRACTIONf_dihedral_angle_d15.5344370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.42730.35151680.27942769293773
2.4273-2.45580.37791520.29272794294674
2.4558-2.48580.37911550.29212881303674
2.4858-2.51720.37651560.29072809296575
2.5172-2.55040.37041450.27352862300775
2.5504-2.58530.39091290.27472957308676
2.5853-2.62220.34251480.2412843299175
2.6222-2.66140.25861630.24212875303877
2.6614-2.7030.32881660.25222992315877
2.703-2.74730.32571330.23672931306478
2.7473-2.79460.33331530.22773006315979
2.7946-2.84550.27881650.21923051321680
2.8455-2.90020.27381640.22423008317279
2.9002-2.95940.30981540.23313054320880
2.9594-3.02370.30881940.22193008320280
3.0237-3.09410.29351790.21863053323280
3.0941-3.17140.27721840.18753027321181
3.1714-3.25720.25831880.17633098328681
3.2572-3.3530.23061730.16553030320381
3.353-3.46120.23411620.16643059322180
3.4612-3.58490.25361560.15173066322281
3.5849-3.72840.19371630.15453111327481
3.7284-3.8980.19911490.15323107325681
3.898-4.10350.22361580.15323084324281
4.1035-4.36050.19751590.15292991315080
4.3605-4.6970.20211410.16063073321480
4.697-5.16930.21261560.1752938309476
5.1693-5.91660.25761660.20192971313779
5.9166-7.45130.21981730.19573253342685
7.4513-54.72270.21591780.19013010318880

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