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- PDB-5yp1: Crystal structure of dipeptidyl peptidase IV (DPP IV) from Pseudo... -

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Basic information

Entry
Database: PDB / ID: 5yp1
TitleCrystal structure of dipeptidyl peptidase IV (DPP IV) from Pseudoxanthomonas mexicana WO24
ComponentsDipeptidyl aminopeptidase 4
KeywordsHYDROLASE / DAP IV / Clan SC S9 / peptidase / DPP4 / DPP8 / DPP9
Function / homology
Function and homology information


dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / aminopeptidase activity / serine-type peptidase activity / proteolysis involved in protein catabolic process / periplasmic space / protein homodimerization activity / identical protein binding / cytoplasm
Similarity search - Function
Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Dipeptidyl aminopeptidase 4
Similarity search - Component
Biological speciesPseudoxanthomonas mexicana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsRoppongi, S. / Suzuki, Y. / Tateoka, C. / Fuimoto, M. / Morisawa, S. / Iizuka, I. / Nakamura, A. / Honma, N. / Shida, Y. / Ogasawara, W. ...Roppongi, S. / Suzuki, Y. / Tateoka, C. / Fuimoto, M. / Morisawa, S. / Iizuka, I. / Nakamura, A. / Honma, N. / Shida, Y. / Ogasawara, W. / Tanaka, N. / Sakamoto, Y. / Nonaka, T.
Funding support Japan, 10items
OrganizationGrant numberCountry
MEXT16K08322 Japan
MEXT25462872 Japan
MEXT16H04902 Japan
MEXT17H03790 Japan
Protein Institute, Osaka Univ.CR1405, CR1505, CR1605, CR1705 Japan
Protein Institute, Osaka Univ.2013A6822, 2013B 6822, 2014A6924, 2014B6924, 2015A6521, 2015B6521, 2016A6620, 2016B6620, 2017A6721, 2017B6721 Japan
KEK2011G090, 2013G138, 2017G162 Japan
AMED Japan
Takeda Foundation Japan
Nagai Foundation Japan
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues.
Authors: Roppongi, S. / Suzuki, Y. / Tateoka, C. / Fujimoto, M. / Morisawa, S. / Iizuka, I. / Nakamura, A. / Honma, N. / Shida, Y. / Ogasawara, W. / Tanaka, N. / Sakamoto, Y. / Nonaka, T.
History
DepositionNov 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: 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 1.2Nov 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

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Assembly

Deposited unit
A: Dipeptidyl aminopeptidase 4
B: Dipeptidyl aminopeptidase 4
C: Dipeptidyl aminopeptidase 4
D: Dipeptidyl aminopeptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,5945
Polymers329,5024
Non-polymers921
Water10,971609
1
A: Dipeptidyl aminopeptidase 4
B: Dipeptidyl aminopeptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,8433
Polymers164,7512
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-19 kcal/mol
Surface area54040 Å2
MethodPISA
2
C: Dipeptidyl aminopeptidase 4
D: Dipeptidyl aminopeptidase 4


Theoretical massNumber of molelcules
Total (without water)164,7512
Polymers164,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-17 kcal/mol
Surface area55040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.730, 326.190, 71.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Dipeptidyl aminopeptidase 4 / Dipeptidyl aminopeptidase IV / DAP IV


Mass: 82375.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoxanthomonas mexicana (bacteria) / Strain: WO24 / Gene: dap4 / Plasmid: pUC19 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q6F3I7, dipeptidyl-peptidase IV
#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.: 609 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsResidue M12I is mutagenesis according to sequence database UniportKB Q6F3I7 (DAP4_PSEMX).

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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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 10% PEG 6000, 5% 2-Methyl-2,4-pentanediol

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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 315r / Detector: CCD / Date: Apr 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.47→55.15 Å / Num. obs: 125591 / % possible obs: 99.9 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.049 / Rrim(I) all: 0.135 / Net I/σ(I): 14
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 5 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 2 / Num. unique obs: 6043 / CC1/2: 0.643 / Rpim(I) all: 0.404 / Rrim(I) all: 0.932 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia20.5.48data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ECF

2ecf


Resolution: 2.47→40 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.877 / SU B: 11.783 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.488 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 6289 5 %RANDOM
Rwork0.21733 ---
obs0.22066 119191 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.745 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å20 Å20 Å2
2---2.66 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.47→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22075 0 6 609 22690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01922635
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220665
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.95330798
X-RAY DIFFRACTIONr_angle_other_deg1.052347741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1152818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44523.0671050
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.855153546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.05615190
X-RAY DIFFRACTIONr_chiral_restr0.0970.23350
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02125551
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024927
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_it3.1694.43711295
X-RAY DIFFRACTIONr_mcbond_other3.1694.43711294
X-RAY DIFFRACTIONr_mcangle_it4.9836.64414106
X-RAY DIFFRACTIONr_mcangle_other4.9826.64414107
X-RAY DIFFRACTIONr_scbond_it2.8944.62511339
X-RAY DIFFRACTIONr_scbond_other2.8934.62511339
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5916.82916693
X-RAY DIFFRACTIONr_long_range_B_refined7.20350.37524675
X-RAY DIFFRACTIONr_long_range_B_other7.20350.37624676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.47→2.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 475 -
Rwork0.317 8554 -
obs--98.29 %

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