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- PDB-8grt: Small Dipeptide Analogues developed by Co-crystal Structure of St... -

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Basic information

Entry
Database: PDB / ID: 8grt
TitleSmall Dipeptide Analogues developed by Co-crystal Structure of Stenotrophomonas maltophilia Dipeptidyl Peptidase 7
ComponentsDipeptidyl-peptidase
KeywordsHYDROLASE / S46 / DPP / aminopeptidase / antibiotics / NFGNR / NFGNB / sepsis / pneumonia
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / serine-type aminopeptidase activity / dipeptidyl-peptidase activity / peptide catabolic process / proteolysis
Similarity search - Function
Peptidase S46 / Peptidase S46 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID / TYROSINE / Dipeptidyl-peptidase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsYasumitsu, S. / Koushi, H. / Akihiro, N. / Yoshiyuki, Y. / Wataru, O. / Mizuki, S. / Saori, R. / Nobutada, T. / Anna, M. / Keiko, H. / Tsuda, Y.
Funding support Japan, 7items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K8322 Japan
Japan Society for the Promotion of Science (JSPS)16H04902 Japan
Japan Society for the Promotion of Science (JSPS)17H03790 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)2013A6822, 2013B6822, 2014A6924, 2014B6924, 2015A6521, 2015B6521, 2016B6620, 2017A6721, 2017B6721, 2018A6818, 2018B6818, 2019A6917, 2019B6917, 2020A6517 Japan
Japan Agency for Medical Research and Development (AMED)BINDS 0026 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)21K09913 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)21K06071 Japan
CitationJournal: To Be Published
Title: Small Dipeptide Analogues Generated by Co-crystal Structure of Bacterial Dipeptidyl Peptidase 7 to Defeat Stenotrophomonas maltophilia
Authors: Koushi, H. / Yasumitsu, S. / Akihiro, N. / Suzuki, Y. / Wataru, O. / Mizuki, S. / Chisato, K. / Saori, R. / Nobutada, T. / Anna, M. / Keiko, H. / Yuko, Y.
History
DepositionSep 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl-peptidase
B: Dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,8286
Polymers156,1232
Non-polymers7054
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-7 kcal/mol
Surface area56370 Å2
Unit cell
Length a, b, c (Å)67.200, 74.250, 154.590
Angle α, β, γ (deg.)90.000, 95.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dipeptidyl-peptidase


Mass: 78061.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain R551-3) (bacteria)
Strain: R551-3 / Cell: Bacteria / Gene: Smal_0807 / Plasmid: pET22b
Details (production host): Full synthetic and codon optimised
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B4SLK2, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Chemical ChemComp-ALC / 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID


Type: L-peptide linking / Mass: 171.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG 8000, 200mM Amm. Acetate, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 26, 2016
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.59→34.58 Å / Num. obs: 47008 / % possible obs: 99 % / Redundancy: 3.7 % / Biso Wilson estimate: 35.788 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.066 / Rrim(I) all: 0.128 / Net I/σ(I): 10.4
Reflection shellResolution: 2.59→2.63 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.565 / Num. unique obs: 1999 / CC1/2: 0.727 / Rpim(I) all: 0.361 / % possible all: 84.8

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Processing

Software
NameVersionClassification
XDS20161205data reduction
xia20.5.161data reduction
DIALS1.4.1data reduction
PHASER2.8.3phasing
REFMAC5.8.0352refinement
Coot0.9.8.3model building
BUCCANEERmodel building
PHENIX1.18.2-3874model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DKB

7dkb


Resolution: 2.59→30.002 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.509 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / ESU R: 1.486 / ESU R Free: 0.317
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 2287 4.868 %Random selection
Rwork0.1754 44694 --
all0.179 ---
obs-46981 98.895 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.587 Å2-0 Å2-0.075 Å2
2--0.246 Å2-0 Å2
3----0.807 Å2
Refinement stepCycle: LAST / Resolution: 2.59→30.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10701 0 0 207 10908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01210933
X-RAY DIFFRACTIONr_bond_other_d0.0020.01610015
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.64614817
X-RAY DIFFRACTIONr_angle_other_deg0.5351.57223333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31451391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.014562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.255101784
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.91310490
X-RAY DIFFRACTIONr_chiral_restr0.0610.21605
X-RAY DIFFRACTIONr_chiral_restr_other1.4340.216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212631
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022157
X-RAY DIFFRACTIONr_nbd_refined0.2150.22211
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.28741
X-RAY DIFFRACTIONr_nbtor_refined0.1770.25282
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.25853
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.214
X-RAY DIFFRACTIONr_nbd_other0.1560.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3020.26
X-RAY DIFFRACTIONr_mcbond_it3.0074.0825576
X-RAY DIFFRACTIONr_mcbond_other3.0074.0825574
X-RAY DIFFRACTIONr_mcangle_it4.6286.1126963
X-RAY DIFFRACTIONr_mcangle_other4.6286.1126963
X-RAY DIFFRACTIONr_scbond_it3.3814.395357
X-RAY DIFFRACTIONr_scbond_other3.3814.395358
X-RAY DIFFRACTIONr_scangle_it5.36.4227854
X-RAY DIFFRACTIONr_scangle_other5.2996.4217855
X-RAY DIFFRACTIONr_lrange_it7.09550.65811942
X-RAY DIFFRACTIONr_lrange_other7.09450.61611936
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.59-2.6570.4681420.3829430.38534480.9050.93789.47220.318
2.657-2.7290.3231480.24532260.24933800.9330.96499.82250.209
2.729-2.8080.281600.20731200.21132880.950.97499.75670.177
2.808-2.8930.291650.19430190.19931890.9550.97799.84320.168
2.893-2.9870.2961510.20529380.20930920.9450.97599.9030.18
2.987-3.0910.3081260.19628850.20130200.9430.97699.7020.177
3.091-3.2060.281340.19227810.19629230.9510.97699.72630.175
3.206-3.3360.2171490.16826110.17127650.970.98399.81920.152
3.336-3.4820.2631190.18825260.19126570.9550.97999.54840.178
3.482-3.6490.231210.1724350.17325640.9670.98299.6880.163
3.649-3.8440.2221280.16923240.17224620.9650.98299.59380.165
3.844-4.0730.2481110.16521880.16923150.960.98399.30890.163
4.073-4.3480.2351060.1520860.15421990.9690.98599.68170.152
4.348-4.6880.209960.14819080.15120130.9750.98799.55290.156
4.688-5.1230.1991010.13618050.13919080.9770.9999.89520.143
5.123-5.7070.199870.16316150.16517070.9780.98799.70710.168
5.707-6.5510.256870.18114260.18515160.9660.98299.80210.185
6.551-7.9290.214690.13612390.1413090.9750.9999.92360.146
7.929-10.8410.147540.1089920.1110500.9860.99399.6190.131
10.841-30.0020.198330.1816270.1826610.9770.98499.84870.213

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