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- PDB-4y01: Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyr... -

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Basic information

Entry
Database: PDB / ID: 4y01
TitleCrystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis
ComponentsPeptidase S46
KeywordsHYDROLASE
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
: / Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.46 Å
AuthorsSakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Nonaka, T. / Ogasawara, W. / Tanaka, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25462872 Japan
CitationJournal: Sci Rep / Year: 2015
Title: Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity.
Authors: Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Inaka, K. / Tanaka, H. / Yamada, M. / Ohta, K. / Gouda, H. / Nonaka, T. / Ogasawara, W. / Tanaka, N.
History
DepositionFeb 5, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase S46
B: Peptidase S46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,4353
Polymers166,3432
Non-polymers921
Water3,351186
1
A: Peptidase S46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2642
Polymers83,1721
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidase S46


Theoretical massNumber of molelcules
Total (without water)83,1721
Polymers83,1721
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.788, 115.486, 147.570
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 Peptidase S46


Mass: 83171.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: EG14_04230 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: A0A076NW73, UniProt: B2RID1*PLUS
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: BICINE pH 9.0, sodium chloride, PEG MME 550

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 20, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.46→40 Å / Num. obs: 62234 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rsym value: 0.11 / Net I/σ(I): 12.6
Reflection shellResolution: 2.46→2.52 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data processing
SHARPphasing
ARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.46→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.339 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.43 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23339 2980 4.8 %RANDOM
Rwork0.18415 ---
obs0.1866 58784 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--2.1 Å20 Å2
3----1.53 Å2
Refinement stepCycle: 1 / Resolution: 2.46→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11216 0 6 186 11408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01911473
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210814
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.96915495
X-RAY DIFFRACTIONr_angle_other_deg1.069324866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07951396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20723.931580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.495151862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5141590
X-RAY DIFFRACTIONr_chiral_restr0.0990.21623
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02113080
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022706
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_it2.8973.8415590
X-RAY DIFFRACTIONr_mcbond_other2.8973.845589
X-RAY DIFFRACTIONr_mcangle_it4.4715.7556984
X-RAY DIFFRACTIONr_mcangle_other4.4715.7566985
X-RAY DIFFRACTIONr_scbond_it3.64.2595883
X-RAY DIFFRACTIONr_scbond_other3.5974.2595883
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7066.2028512
X-RAY DIFFRACTIONr_long_range_B_refined7.40730.50713059
X-RAY DIFFRACTIONr_long_range_B_other7.40830.51713031
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 187 -
Rwork0.286 3609 -
obs--90.17 %

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