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- PDB-4wjl: Structure of human dipeptidyl peptidase 10 (DPPY): a modulator of... -

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Basic information

Entry
Database: PDB / ID: 4wjl
TitleStructure of human dipeptidyl peptidase 10 (DPPY): a modulator of neuronal Kv4 channels
ComponentsInactive dipeptidyl peptidase 10
KeywordsMEMBRANE PROTEIN / inactive dipeptidyl peptidase 10 / DPP4 structure homologue / alpha/beta hydrolase / beta-propeller
Function / homology
Function and homology information


regulation of potassium ion transmembrane transport / potassium channel regulator activity / voltage-gated potassium channel complex / serine-type peptidase activity / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / transmembrane transporter binding / membrane / plasma membrane
Similarity search - Function
: / 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 ...: / 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
Inactive dipeptidyl peptidase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.4 Å
AuthorsBezerra, G.A. / Dobrovetsky, E. / Seitova, A. / Fedosyuk, S. / Dhe-Paganon, S. / Gruber, K.
CitationJournal: Sci Rep / Year: 2015
Title: Structure of human dipeptidyl peptidase 10 (DPPY): a modulator of neuronal Kv4 channels.
Authors: Bezerra, G.A. / Dobrovetsky, E. / Seitova, A. / Fedosyuk, S. / Dhe-Paganon, S. / Gruber, K.
History
DepositionSep 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inactive dipeptidyl peptidase 10
B: Inactive dipeptidyl peptidase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,72611
Polymers165,2332
Non-polymers3,4939
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint27 kcal/mol
Surface area60840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.910, 143.730, 176.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 67:407 or resseq 412:782 )
211chain B and (resseq 67:407 or resseq 412:782 )

NCS oper: (Code: given
Matrix: (-0.999919, -0.003172, 0.012346), (0.006281, 0.720166, 0.693774), (-0.011091, 0.693795, -0.720087)
Vector: -40.510399, 36.554501, -90.827202)

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Components

#1: Protein Inactive dipeptidyl peptidase 10 / Dipeptidyl peptidase IV-related protein 3 / DPRP-3 / Dipeptidyl peptidase X / DPP X / Dipeptidyl ...Dipeptidyl peptidase IV-related protein 3 / DPRP-3 / Dipeptidyl peptidase X / DPP X / Dipeptidyl peptidase-like protein 2 / DPL2


Mass: 82616.289 Da / Num. of mol.: 2 / Fragment: UNP residues 65-783
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP10, DPRP3, KIAA1492 / Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9 / References: UniProt: Q8N608
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 3.1 Å3/Da / Density % sol: 60.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Crystals formed within 2-4 weeks using 100 micrometers of reservoir solution consisting of 20%(w/v) PEG 1500, 0.2 M MgCl2, 0.1 M sodium cacodylate pH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97943 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 3.4→111.388 Å / Num. all: 29019 / Num. obs: 29019 / % possible obs: 99.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 74.4 Å2 / Rpim(I) all: 0.108 / Rrim(I) all: 0.251 / Rsym value: 0.226 / Net I/av σ(I): 3.096 / Net I/σ(I): 6.8 / Num. measured all: 149063
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3.4-3.5850.7750.92063041500.3780.7752.399.9
3.58-3.850.5761.21979439350.2790.5763.199.9
3.8-4.065.10.4051.71902337250.1950.4054.299.9
4.06-4.395.20.2792.71811534730.1320.2795.9100
4.39-4.815.30.2033.61709532280.0960.2038100
4.81-5.385.30.1694.41548329200.080.1698.7100
5.38-6.215.30.1744.21361825880.0830.1748.1100
6.21-7.65.20.1375.31149022180.0660.1379.4100
7.6-10.755.10.05710.7895517590.0280.05715.9100
10.75-66.5464.80.0539.2486010230.0260.05318.299.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.99 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å66.55 Å
Translation3.5 Å66.55 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7_650)refinement
SCALA3.3.9data scaling
PHASER2.1.4phasing
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XFD

1xfd


Resolution: 3.4→66.546 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 1476 5.1 %
Rwork0.2074 --
obs0.2092 28967 99.91 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.006 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.2794 Å20 Å20 Å2
2--9.6109 Å2-0 Å2
3----5.3315 Å2
Refinement stepCycle: LAST / Resolution: 3.4→66.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11600 0 229 0 11829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812146
X-RAY DIFFRACTIONf_angle_d1.36216474
X-RAY DIFFRACTIONf_dihedral_angle_d20.864530
X-RAY DIFFRACTIONf_chiral_restr0.1021856
X-RAY DIFFRACTIONf_plane_restr0.0072053
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A5752X-RAY DIFFRACTIONPOSITIONAL
12B5752X-RAY DIFFRACTIONPOSITIONAL0.052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.50980.31341160.28042462X-RAY DIFFRACTION100
3.5098-3.63520.29221310.25522425X-RAY DIFFRACTION100
3.6352-3.78070.30781330.252470X-RAY DIFFRACTION100
3.7807-3.95280.26021320.21792458X-RAY DIFFRACTION100
3.9528-4.16110.24421360.20742490X-RAY DIFFRACTION100
4.1611-4.42180.24011290.18012480X-RAY DIFFRACTION100
4.4218-4.76310.17921460.1632489X-RAY DIFFRACTION100
4.7631-5.24230.21691370.16542479X-RAY DIFFRACTION100
5.2423-6.00040.24991500.19422512X-RAY DIFFRACTION100
6.0004-7.55820.22791260.22412560X-RAY DIFFRACTION100
7.5582-66.55850.23631400.21762666X-RAY DIFFRACTION100

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