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- PDB-6qzv: DPP9 bound to a dipeptide (MP) from the N-terminus of BRCA2 -

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Basic information

Entry
Database: PDB / ID: 6qzv
TitleDPP9 bound to a dipeptide (MP) from the N-terminus of BRCA2
Components
  • Dipeptidyl peptidase 9
  • 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 / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding ...dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding / nucleus / cytosol
Similarity search - Function
Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family ...Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / : / 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 / Mainly Beta
Similarity search - Domain/homology
Dipeptidyl peptidase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
A: Dipeptidyl peptidase 9
B: Dipeptidyl peptidase 9
C: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
E: MET-PRO
F: MET-PRO
G: MET-PRO
H: MET-PRO


Theoretical massNumber of molelcules
Total (without water)411,4948
Polymers411,4948
Non-polymers00
Water724
1
A: Dipeptidyl peptidase 9
B: Dipeptidyl peptidase 9
E: MET-PRO
F: MET-PRO


Theoretical massNumber of molelcules
Total (without water)205,7474
Polymers205,7474
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-25 kcal/mol
Surface area63390 Å2
MethodPISA
2
C: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
G: MET-PRO
H: MET-PRO


Theoretical massNumber of molelcules
Total (without water)205,7474
Polymers205,7474
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-23 kcal/mol
Surface area63020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.516, 117.219, 163.401
Angle α, β, γ (deg.)90.00, 105.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dipeptidyl peptidase 9 / DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / ...DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / Dipeptidyl peptidase-like protein 9 / DPLP9


Mass: 102627.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP9, DPRP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86TI2, dipeptidyl-peptidase IV
#2: Protein/peptide
MET-PRO


Mass: 246.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 20 mg/ml of protein, 10% PEG 8000, 25% glycerol, 0.16 M calcium acetate, 0.08 M cacodilate pH 6.25. 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: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 3→43.47 Å / Num. obs: 76534 / % possible obs: 87.8 % / Redundancy: 2.65 % / CC1/2: 0.98 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.9
Reflection shellResolution: 3→3.19 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / Num. unique obs: 13092 / CC1/2: 0.93 / % possible all: 88.8

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Processing

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

6eoq


Resolution: 3→43.47 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.828 / SU B: 29.275 / SU ML: 0.533 / Cross valid method: THROUGHOUT / ESU R Free: 0.662 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34517 3827 5 %RANDOM
Rwork0.28573 ---
obs0.28871 72706 88.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.557 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20 Å2-0.23 Å2
2--3.79 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 3→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26312 0 0 4 26316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01327089
X-RAY DIFFRACTIONr_bond_other_d0.0020.01724371
X-RAY DIFFRACTIONr_angle_refined_deg1.121.64436728
X-RAY DIFFRACTIONr_angle_other_deg0.3481.57156654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21853200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11322.0921496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.554154425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.16915160
X-RAY DIFFRACTIONr_chiral_restr0.0460.23305
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0230132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025996
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_it1.1362.74112923
X-RAY DIFFRACTIONr_mcbond_other1.1362.74112922
X-RAY DIFFRACTIONr_mcangle_it2.0364.09916082
X-RAY DIFFRACTIONr_mcangle_other2.0364.09916083
X-RAY DIFFRACTIONr_scbond_it0.8392.80314166
X-RAY DIFFRACTIONr_scbond_other0.8382.80314166
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5264.16620646
X-RAY DIFFRACTIONr_long_range_B_refined3.6730.229418
X-RAY DIFFRACTIONr_long_range_B_other3.6730.20129419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.002→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 283 -
Rwork0.335 5385 -
obs--89.11 %

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