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- PDB-6eop: DPP8 - SLRFLYEG, space group 20 -

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Basic information

Entry
Database: PDB / ID: 6eop
TitleDPP8 - SLRFLYEG, space group 20
Components
  • Dipeptidyl peptidase 8
  • SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
KeywordsHYDROLASE / DPP8
Function / homology
Function and homology information


protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) ...protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / nuclear stress granule / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / dipeptidyl-peptidase IV / septin ring / regulation of calcium ion transmembrane transport / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of cardiac muscle cell contraction / dipeptidyl-peptidase activity / negative regulation of programmed cell death / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / roof of mouth development / SUMOylation of ubiquitinylation proteins / ubiquitin-like protein ligase binding / negative regulation of DNA binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / Regulation of IFNG signaling / nuclear pore / aminopeptidase activity / cellular response to cadmium ion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein-containing complex assembly / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / Formation of Incision Complex in GG-NER / protein tag activity / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / nuclear body / protein stabilization / nuclear speck / immune response / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / nucleolus / enzyme binding / proteolysis / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Ubiquitin homologues ...Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Alpha/Beta hydrolase fold / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
PENTADECANOIC ACID / CITRATE ANION / Small ubiquitin-related modifier 1 / Dipeptidyl peptidase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 8
B: Dipeptidyl peptidase 8
C: Dipeptidyl peptidase 8
D: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
E: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
F: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,67013
Polymers313,6346
Non-polymers1,0377
Water10,665592
1
A: Dipeptidyl peptidase 8
D: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
hetero molecules

A: Dipeptidyl peptidase 8
D: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,03210
Polymers209,0894
Non-polymers9436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area10360 Å2
ΔGint-24 kcal/mol
Surface area64420 Å2
MethodPISA
2
B: Dipeptidyl peptidase 8
C: Dipeptidyl peptidase 8
E: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
F: SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,6548
Polymers209,0894
Non-polymers5654
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-21 kcal/mol
Surface area63180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.830, 246.371, 261.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDEF

#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: 103559.469 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 SER-LEU-ARG-PHE-LEU-TYR-GLU-GLY


Mass: 985.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P63165*PLUS

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Non-polymers , 4 types, 599 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-F15 / PENTADECANOIC ACID / Pentadecylic acid


Mass: 242.397 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H30O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 4.18 Å3/Da / Density % sol: 70.55 %
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: 0.99992 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 2.4→44.62 Å / Num. obs: 203220 / % possible obs: 100 % / Redundancy: 8.44 % / Rsym value: 0.17 / Net I/σ(I): 22.8
Reflection shellResolution: 2.4→2.56 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2.09 / Num. unique obs: 34229 / CC1/2: 0.719 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ORV

1orv


Resolution: 2.4→44.62 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.091 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23663 10161 5 %RANDOM
Rwork0.21358 ---
obs0.21474 193059 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.666 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0 Å2-0 Å2
2--2.84 Å20 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 2.4→44.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20692 0 67 592 21351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01921320
X-RAY DIFFRACTIONr_bond_other_d0.0060.0219874
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9628884
X-RAY DIFFRACTIONr_angle_other_deg0.853345837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09252528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1423.3811044
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28153576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.47915147
X-RAY DIFFRACTIONr_chiral_restr0.0680.23051
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02123871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025078
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_it1.8846.42210148
X-RAY DIFFRACTIONr_mcbond_other1.8846.42210147
X-RAY DIFFRACTIONr_mcangle_it3.2829.62712664
X-RAY DIFFRACTIONr_mcangle_other3.2829.62712665
X-RAY DIFFRACTIONr_scbond_it1.6776.60111172
X-RAY DIFFRACTIONr_scbond_other1.6776.611170
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9349.8116220
X-RAY DIFFRACTIONr_long_range_B_refined5.26271.02822532
X-RAY DIFFRACTIONr_long_range_B_other5.26271.02722532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.531 742 -
Rwork0.496 14110 -
obs--99.39 %

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