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- PDB-6jtc: Crystal structure of dipeptidyl peptidase 11 (DPP11) with SH-5 fr... -

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Basic information

Entry
Database: PDB / ID: 6jtc
TitleCrystal structure of dipeptidyl peptidase 11 (DPP11) with SH-5 from Porphyromonas gingivalis (Space)
ComponentsAsp/Glu-specific dipeptidyl-peptidase
KeywordsHYDROLASE / dipeptidyl aminopeptidase / S46 / perio / Microgravity / antimicrobial
Function / homology
Function and homology information


developmental cell growth / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / serine-type aminopeptidase activity / dipeptidyl-peptidase activity / peptide catabolic process / peptide binding / cell surface / proteolysis
Similarity search - Function
Peptidase S46 / Peptidase S46 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
2-(2-azanylethylamino)-5-nitro-benzoic acid / Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsSakamoto, Y. / Suzuki, Y. / Iizuka, I. / Roppongi, S. / Kushibiki, C. / Nakamura, A. / Ogasawara, W. / Tanaka, N.
Funding support Japan, 9items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25462872 Japan
Japan Society for the Promotion of Science16K08322 Japan
Japan Society for the Promotion of Science18K06629 Japan
Japan Society for the Promotion of Science18K06661 Japan
Japan Society for the Promotion of Science17H03790 Japan
Japan Society for the Promotion of Science16H04902 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)H29-A3 Japan
Japan Agency for Medical Research and Development (AMED)BINDS 0026 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)CR1405-CR1905 Japan
CitationJournal: Sci Rep / Year: 2019
Title: Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase.
Authors: Sakamoto, Y. / Suzuki, Y. / Nakamura, A. / Watanabe, Y. / Sekiya, M. / Roppongi, S. / Kushibiki, C. / Iizuka, I. / Tani, O. / Sakashita, H. / Inaka, K. / Tanaka, H. / Yamada, M. / Ohta, K. / ...Authors: Sakamoto, Y. / Suzuki, Y. / Nakamura, A. / Watanabe, Y. / Sekiya, M. / Roppongi, S. / Kushibiki, C. / Iizuka, I. / Tani, O. / Sakashita, H. / Inaka, K. / Tanaka, H. / Yamada, M. / Ohta, K. / Honma, N. / Shida, Y. / Ogasawara, W. / Nakanishi-Matsui, M. / Nonaka, T. / Gouda, H. / Tanaka, N.
History
DepositionApr 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Asp/Glu-specific dipeptidyl-peptidase
B: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,6355
Polymers164,0922
Non-polymers5423
Water4,053225
1
A: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3633
Polymers82,0461
Non-polymers3172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint0 kcal/mol
Surface area30530 Å2
MethodPISA
2
B: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2712
Polymers82,0461
Non-polymers2251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area30240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.337, 116.960, 148.200
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 Asp/Glu-specific dipeptidyl-peptidase / Dipeptidyl-peptidase 11 / DPP11


Mass: 82046.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria)
Strain: ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561
Gene: dpp11, PGN_0607 / Production host: Escherichia coli (E. coli)
References: UniProt: B2RID1, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-C8O / 2-(2-azanylethylamino)-5-nitro-benzoic acid


Mass: 225.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11N3O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 8.5
Details: 19 %(m/v) PEG 8000,0.18 M magnesium formate, 0.5 mM SH-5, 5 % (v/v) DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.39→116.94 Å / Num. obs: 70956 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 30.999 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.063 / Rrim(I) all: 0.169 / Net I/σ(I): 9.2
Reflection shellResolution: 2.39→2.43 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.283 / Num. unique obs: 3428 / CC1/2: 0.692 / Rpim(I) all: 0.502 / Rrim(I) all: 1.38 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia20.5.576data reduction
DIALS1.10.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y04

4y04


Resolution: 2.39→39.65 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.199 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25275 3516 5 %RANDOM
Rwork0.20228 ---
obs0.20477 67329 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.637 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2--0.34 Å20 Å2
3----2.27 Å2
Refinement stepCycle: 1 / Resolution: 2.39→39.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11216 0 38 225 11479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311505
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710568
X-RAY DIFFRACTIONr_angle_refined_deg1.561.65215541
X-RAY DIFFRACTIONr_angle_other_deg1.2811.58824494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23951396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0922.06670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.631152000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.181590
X-RAY DIFFRACTIONr_chiral_restr0.0680.21434
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213004
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022538
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_it3.1774.3425590
X-RAY DIFFRACTIONr_mcbond_other3.1744.3425589
X-RAY DIFFRACTIONr_mcangle_it4.7886.5096984
X-RAY DIFFRACTIONr_mcangle_other4.7886.5096985
X-RAY DIFFRACTIONr_scbond_it3.6694.735915
X-RAY DIFFRACTIONr_scbond_other3.6694.735916
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.686.9148558
X-RAY DIFFRACTIONr_long_range_B_refined7.47649.72312941
X-RAY DIFFRACTIONr_long_range_B_other7.47649.72512941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 253 -
Rwork0.304 4873 -
obs--99.51 %

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