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- PDB-7dke: Stenotrophomonas maltophilia DPP7 in complex with Phe-Tyr -

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Basic information

Entry
Database: PDB / ID: 7dke
TitleStenotrophomonas maltophilia DPP7 in complex with Phe-Tyr
ComponentsDipeptidyl-peptidase
KeywordsHYDROLASE / dipeptidyl aminopeptidase / S46 / AMR / Microgravity / antimicrobial / chymotrypsin / serine protease
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
PHENYLALANINE / TYROSINE / Dipeptidyl-peptidase
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsSakamoto, Y. / Nakamura, A. / Suzuki, Y. / Honma, N. / Roppongi, S. / Kushibiki, C. / Yonezawa, N. / Takahashi, M. / Shida, Y. / Gouda, H. ...Sakamoto, Y. / Nakamura, A. / Suzuki, Y. / Honma, N. / Roppongi, S. / Kushibiki, C. / Yonezawa, N. / Takahashi, M. / Shida, Y. / Gouda, H. / Nonaka, T. / Ogasawara, W. / Tanaka, N.
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
Ministry of Education, Culture, Sports, Science and Technology (Japan)CR1405-CR1905 Japan
Japan Agency for Medical Research and Development (AMED)BINDS-0026 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)2017G162 Japan
CitationJournal: Sci Rep / Year: 2021
Title: Structural basis for an exceptionally strong preference for asparagine residue at the S2 subsite of Stenotrophomonas maltophilia dipeptidyl peptidase 7.
Authors: Nakamura, A. / Suzuki, Y. / Sakamoto, Y. / Roppongi, S. / Kushibiki, C. / Yonezawa, N. / Takahashi, M. / Shida, Y. / Gouda, H. / Nonaka, T. / Tanaka, N. / Ogasawara, W.
History
DepositionNov 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Nov 6, 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)157,27611
Polymers156,1232
Non-polymers1,1539
Water15,511861
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-7 kcal/mol
Surface area55540 Å2
2
A: Dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7767
Polymers78,0611
Non-polymers7156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-1 kcal/mol
Surface area28240 Å2
MethodPISA
3
B: Dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5004
Polymers78,0611
Non-polymers4383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-1 kcal/mol
Surface area28320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.035, 74.555, 153.868
Angle α, β, γ (deg.)90.000, 94.437, 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 / Gene: Smal_0807 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold(DE3)
References: UniProt: B4SLK2, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M Ca Acetate, 20%w/v PEG 8000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.91→43.13 Å / Num. obs: 118877 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.163 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.064 / Rrim(I) all: 0.17 / Net I/σ(I): 7
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.012 / Mean I/σ(I) obs: 2 / Num. unique obs: 5580 / CC1/2: 0.631 / Rpim(I) all: 0.421 / % possible all: 93.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia20.5.764data reduction
DIALS1.12.2data scaling
REFMAC5.8.0267phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DKB

7dkb


Resolution: 1.91→40.003 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.97 / SU ML: 0.115 / Cross valid method: FREE R-VALUE / ESU R: 0.168 / ESU R Free: 0.157
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2511 5862 4.932 %
Rwork0.2073 112986 -
all0.209 --
obs-118848 99.685 %
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: 33.301 Å2
Baniso -1Baniso -2Baniso -3
1--1.982 Å2-0 Å2-1.009 Å2
2--0.302 Å20 Å2
3---1.814 Å2
Refinement stepCycle: LAST / Resolution: 1.91→40.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10658 0 78 861 11597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01310973
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710428
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.64114864
X-RAY DIFFRACTIONr_angle_other_deg1.3511.58523970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5451396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58322.926557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.024151790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.061562
X-RAY DIFFRACTIONr_chiral_restr0.0730.21379
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022554
X-RAY DIFFRACTIONr_nbd_refined0.2070.22412
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.29942
X-RAY DIFFRACTIONr_nbtor_refined0.1680.25372
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.25288
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2782
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.218
X-RAY DIFFRACTIONr_nbd_other0.1460.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2210.224
X-RAY DIFFRACTIONr_mcbond_it2.6463.3125593
X-RAY DIFFRACTIONr_mcbond_other2.6433.3125592
X-RAY DIFFRACTIONr_mcangle_it3.6074.9626986
X-RAY DIFFRACTIONr_mcangle_other3.6074.9626987
X-RAY DIFFRACTIONr_scbond_it3.1143.6335380
X-RAY DIFFRACTIONr_scbond_other3.1143.6335381
X-RAY DIFFRACTIONr_scangle_it4.715.2997878
X-RAY DIFFRACTIONr_scangle_other4.7095.2997879
X-RAY DIFFRACTIONr_lrange_it6.1539.49912720
X-RAY DIFFRACTIONr_lrange_other6.06139.27812505
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
1.91-1.9590.3014190.28181040.28287350.8180.83697.5730.268
1.959-2.0130.3044110.26381780.26585920.8330.8699.96510.249
2.013-2.0710.2673730.24379240.24482990.8820.88799.97590.231
2.071-2.1350.2724080.22776300.2380400.8880.90699.97510.213
2.135-2.2050.2334040.20773820.20977880.9080.92399.97430.194
2.205-2.2820.243950.20271820.20475840.9190.92699.90770.188
2.282-2.3680.2683930.19168760.19572710.9010.93199.97250.18
2.368-2.4640.2473530.19666960.19870630.9150.92699.80180.186
2.464-2.5730.2473340.18764230.1967590.9160.93599.97040.183
2.573-2.6980.2713240.20260950.20664390.8990.92299.68940.203
2.698-2.8430.2472960.19358560.19561640.9150.93599.80530.2
2.843-3.0150.2532910.19255260.19558180.9170.93499.98280.205
3.015-3.2220.2232650.18552140.18754840.9350.94399.90880.203
3.222-3.4780.2212570.18848510.1951100.9350.94399.96090.213
3.478-3.8070.2442020.19145110.19347180.9150.93499.8940.223
3.807-4.2520.2252000.18840890.1942930.9390.94899.90680.228
4.252-4.90.2461670.18635970.18837690.9310.95399.86730.234
4.9-5.9790.2441620.21130660.21232330.9380.94699.84530.26
5.979-8.3630.2611250.24223960.24325300.9140.9299.64430.289
8.363-40.0030.309820.29613820.29714940.8920.91497.9920.359

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