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- PDB-6qzw: DPP8 bound to a dipeptide (MP) from the N-terminus of BRCA2 -

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Basic information

Entry
Database: PDB / ID: 6qzw
TitleDPP8 bound to a dipeptide (MP) from the N-terminus of BRCA2
Components
  • Dipeptidyl peptidase 8
  • MET-PRO
KeywordsHYDROLASE / DPP8 / DPP9 / BRCA2 / dipeptide
Function / homology
Function and homology information


dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / aminopeptidase activity / serine-type peptidase activity / immune response / apoptotic process / proteolysis / cytosol / cytoplasm
Similarity search - Function
Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Dipeptidyl peptidase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRoss, B. / Geiss-Friedlander, R. / Huber, R.
CitationJournal: Biorxiv / Year: 2020
Title: Dipeptidyl peptidase 9 triggers BRCA2 degradation by the N-degron pathway to promote DNA-damage repair
Authors: Silva-Garcia, M. / Bolgi, O. / Ross, B. / Pilla, E. / Kari, V. / Killisch, M. / Stark, N. / Lenz, C. / Spitzner, M. / Gorrell, M.D. / Grade, M. / Urlaub, H. / Dobbelstein, M. / Huber, R. / Geiss-Friedlander, R.
History
DepositionMar 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Dipeptidyl peptidase 8
A: Dipeptidyl peptidase 8
B: Dipeptidyl peptidase 8
D: MET-PRO
E: MET-PRO
F: MET-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,2127
Polymers311,1896
Non-polymers231
Water36020
1
A: Dipeptidyl peptidase 8
B: Dipeptidyl peptidase 8
D: MET-PRO
E: MET-PRO


Theoretical massNumber of molelcules
Total (without water)207,4594
Polymers207,4594
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Dipeptidyl peptidase 8
F: MET-PRO
hetero molecules

C: Dipeptidyl peptidase 8
F: MET-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,5056
Polymers207,4594
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5830 Å2
ΔGint-44 kcal/mol
Surface area64330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.730, 246.074, 261.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Dipeptidyl peptidase 8 / / DP8 / Dipeptidyl peptidase IV-related protein 1 / DPRP-1 / Dipeptidyl peptidase VIII / DPP VIII / ...DP8 / Dipeptidyl peptidase IV-related protein 1 / DPRP-1 / Dipeptidyl peptidase VIII / DPP VIII / Prolyl dipeptidase DPP8


Mass: 103483.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP8, DPRP1, MSTP097, MSTP135, MSTP141 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6V1X1, dipeptidyl-peptidase IV
#2: Protein/peptide MET-PRO


Mass: 246.326 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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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: 4.21 Å3/Da / Density % sol: 70.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: 10 mg/ml of protein, 0.46 M Na citrate. Drops are set in a 1:1 ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→44.58 Å / Num. obs: 86559 / % possible obs: 99.9 % / Redundancy: 8.37 % / CC1/2: 0.99 / Rmerge(I) obs: 0.134 / Net I/σ(I): 17.2
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6331 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EOO

6eoo


Resolution: 3.2→44.58 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.409 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 3.866 / ESU R Free: 0.365 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22478 4323 5 %RANDOM
Rwork0.18395 ---
obs0.18599 82126 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 84.864 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-0 Å2
2--3.55 Å20 Å2
3----3.24 Å2
Refinement stepCycle: 1 / Resolution: 3.2→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20388 0 1 20 20409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01320946
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719035
X-RAY DIFFRACTIONr_angle_refined_deg0.9841.64728404
X-RAY DIFFRACTIONr_angle_other_deg0.2841.57244208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85652490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20221.7691170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.652153528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.71115144
X-RAY DIFFRACTIONr_chiral_restr0.040.22646
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0223325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024635
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1918.93910005
X-RAY DIFFRACTIONr_mcbond_other3.1918.93910004
X-RAY DIFFRACTIONr_mcangle_it5.34813.40312480
X-RAY DIFFRACTIONr_mcangle_other5.34813.40312481
X-RAY DIFFRACTIONr_scbond_it3.1539.30410941
X-RAY DIFFRACTIONr_scbond_other3.1539.30410941
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.44513.79815924
X-RAY DIFFRACTIONr_long_range_B_refined8.49322469
X-RAY DIFFRACTIONr_long_range_B_other8.49322470
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 313 -
Rwork0.345 5954 -
obs--99.37 %

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