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- PDB-6eos: DPP8 - Apo, space group 19 -

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Basic information

Entry
Database: PDB / ID: 6eos
TitleDPP8 - Apo, space group 19
ComponentsDipeptidyl peptidase 8
KeywordsHYDROLASE / DPP8
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 / cytoplasm / 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 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / refine_hist
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine_hist.d_res_low
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 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 8
C: Dipeptidyl peptidase 8
D: Dipeptidyl peptidase 8
E: Dipeptidyl peptidase 8
F: Dipeptidyl peptidase 8
B: Dipeptidyl peptidase 8


Theoretical massNumber of molelcules
Total (without water)620,9006
Polymers620,9006
Non-polymers00
Water2,252125
1
A: Dipeptidyl peptidase 8
B: Dipeptidyl peptidase 8


Theoretical massNumber of molelcules
Total (without water)206,9672
Polymers206,9672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-17 kcal/mol
Surface area64000 Å2
MethodPISA
2
C: Dipeptidyl peptidase 8
D: Dipeptidyl peptidase 8


Theoretical massNumber of molelcules
Total (without water)206,9672
Polymers206,9672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-17 kcal/mol
Surface area65520 Å2
MethodPISA
3
E: Dipeptidyl peptidase 8
F: Dipeptidyl peptidase 8


Theoretical massNumber of molelcules
Total (without water)206,9672
Polymers206,9672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-15 kcal/mol
Surface area64680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.122, 266.778, 268.092
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 4.27 Å3/Da / Density % sol: 71.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Na Citrate 0.46M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 3.1→44.4 Å / Num. obs: 191919 / % possible obs: 99.9 % / Redundancy: 8.36 % / Rsym value: 0.18 / Net I/σ(I): 13.8
Reflection shellResolution: 3.1→3.3 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.44 / Num. unique obs: 32519 / CC1/2: 0.66 / % possible all: 99.8

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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: 3.1→44.4 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.899 / SU B: 27.745 / SU ML: 0.435 / Cross valid method: THROUGHOUT / ESU R: 1.045 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28287 9593 5 %RANDOM
Rwork0.24723 ---
obs0.249 182267 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.625 Å2
Baniso -1Baniso -2Baniso -3
1-4.11 Å20 Å20 Å2
2--4.24 Å2-0 Å2
3----8.35 Å2
Refinement stepCycle: 1 / Resolution: 3.1→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39873 0 0 125 39998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01940983
X-RAY DIFFRACTIONr_bond_other_d0.0060.0238077
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.95655609
X-RAY DIFFRACTIONr_angle_other_deg0.86387831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32854887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23523.5491998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.861156849
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.60215261
X-RAY DIFFRACTIONr_chiral_restr0.0660.25912
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02146017
X-RAY DIFFRACTIONr_gen_planes_other0.0010.029738
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_it1.78210.1119617
X-RAY DIFFRACTIONr_mcbond_other1.78210.1119616
X-RAY DIFFRACTIONr_mcangle_it3.26715.15824481
X-RAY DIFFRACTIONr_mcangle_other3.26715.15824482
X-RAY DIFFRACTIONr_scbond_it1.19210.19521366
X-RAY DIFFRACTIONr_scbond_other1.19210.19521367
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.38515.24331129
X-RAY DIFFRACTIONr_long_range_B_refined5.22843577
X-RAY DIFFRACTIONr_long_range_B_other5.22743576
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.101→3.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 697 -
Rwork0.415 13249 -
obs--99.69 %

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