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- PDB-6eoq: DPP9 - Apo -

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Basic information

Entry
Database: PDB / ID: 6eoq
TitleDPP9 - Apo
ComponentsDipeptidyl peptidase 9
KeywordsHYDROLASE / DPP9
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha 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.R. / Huber, R.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer.
Authors: Ross, B. / Krapp, S. / Augustin, M. / Kierfersauer, R. / Arciniega, M. / Geiss-Friedlander, R. / Huber, R.
History
DepositionOct 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: 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
Item: _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


Theoretical massNumber of molelcules
Total (without water)396,8534
Polymers396,8534
Non-polymers00
Water1,47782
1
A: Dipeptidyl peptidase 9
C: Dipeptidyl peptidase 9


Theoretical massNumber of molelcules
Total (without water)198,4262
Polymers198,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-15 kcal/mol
Surface area61580 Å2
MethodPISA
2
B: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9


Theoretical massNumber of molelcules
Total (without water)198,4262
Polymers198,4262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-14 kcal/mol
Surface area61800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.370, 118.020, 164.460
Angle α, β, γ (deg.)90.00, 105.49, 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: 99213.211 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10%PEG 8000, 25% Glycerol, 0.16M Calcium Acetate, 0.08M Caodilate pH6.25,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 3→49.26 Å / Num. obs: 88848 / % possible obs: 99.8 % / Redundancy: 13.57 % / Rsym value: 0.55 / Net I/σ(I): 5.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ORV

1orv


Resolution: 3→49.26 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.87 / SU B: 31.069 / SU ML: 0.549 / Cross valid method: THROUGHOUT / ESU R Free: 0.555 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33414 4443 5 %RANDOM
Rwork0.273 ---
obs0.27605 84415 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.544 Å2
Baniso -1Baniso -2Baniso -3
1--4.61 Å20 Å2-0.81 Å2
2--6.68 Å20 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 3→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24880 0 0 82 24962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01925618
X-RAY DIFFRACTIONr_bond_other_d0.0020.0223735
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.94334746
X-RAY DIFFRACTIONr_angle_other_deg1.999354683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65953016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47223.5981248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.597154166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.88315140
X-RAY DIFFRACTIONr_chiral_restr0.0760.23656
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02128682
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026240
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_it2.5695.3812208
X-RAY DIFFRACTIONr_mcbond_other2.5695.3812207
X-RAY DIFFRACTIONr_mcangle_it4.2968.0515176
X-RAY DIFFRACTIONr_mcangle_other4.2968.05115177
X-RAY DIFFRACTIONr_scbond_it2.2945.58313410
X-RAY DIFFRACTIONr_scbond_other2.2945.58413411
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9628.27619571
X-RAY DIFFRACTIONr_long_range_B_refined6.759.34626977
X-RAY DIFFRACTIONr_long_range_B_other6.70259.3526978
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 326 -
Rwork0.389 6196 -
obs--99.95 %

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