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- PDB-4y04: Crystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyr... -

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Basic information

Entry
Database: PDB / ID: 4y04
TitleCrystal structure of dipeptidyl peptidase 11 (DPP11) from Porphyromonas gingivalis (Space)
ComponentsPeptidase S46
KeywordsHYDROLASE / Space / WT
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 / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsSakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Inaka, K. / Tanaka, H. / Yamada, M. / Ohta, K. ...Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Inaka, K. / Tanaka, H. / Yamada, M. / Ohta, K. / 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 ...diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidase S46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2164
Polymers82,0461
Non-polymers1703
Water12,538696
1
A: Peptidase S46
hetero molecules

A: Peptidase S46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,4338
Polymers164,0922
Non-polymers3416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)99.140, 103.280, 175.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Peptidase S46


Mass: 82046.203 Da / Num. of mol.: 1
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 696 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 293 K / Method: liquid diffusion
Details: tri-potassium citrate, PEG 8000 Crystallisation under micro gravity at ISS Kibo.

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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: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.66→40 Å / Num. obs: 105914 / % possible obs: 99.6 % / Redundancy: 6.2 % / Rsym value: 0.05 / Net I/σ(I): 19.8
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.5 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y01

4y01


Resolution: 1.66→40 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.548 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22473 5266 5 %RANDOM
Rwork0.18613 ---
obs0.18807 100599 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.641 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2---1.1 Å20 Å2
3---2.88 Å2
Refinement stepCycle: 1 / Resolution: 1.66→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5522 0 8 696 6226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195664
X-RAY DIFFRACTIONr_bond_other_d0.0020.025348
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.9567649
X-RAY DIFFRACTIONr_angle_other_deg1.126312294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4535687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08923.776286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04715988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7351546
X-RAY DIFFRACTIONr_chiral_restr0.130.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216451
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021343
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_it2.7682.9492751
X-RAY DIFFRACTIONr_mcbond_other2.7672.9482750
X-RAY DIFFRACTIONr_mcangle_it3.6174.4113437
X-RAY DIFFRACTIONr_mcangle_other3.6184.4123438
X-RAY DIFFRACTIONr_scbond_it3.8313.3512913
X-RAY DIFFRACTIONr_scbond_other3.833.3512913
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4734.8594213
X-RAY DIFFRACTIONr_long_range_B_refined6.89225.4817233
X-RAY DIFFRACTIONr_long_range_B_other6.71224.776872
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 367 -
Rwork0.326 7398 -
obs--99.92 %

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