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- PDB-7a3f: Crystal structure of apo DPP9 -

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Basic information

Entry
Database: PDB / ID: 7a3f
TitleCrystal structure of apo DPP9
ComponentsDipeptidyl peptidase 9
KeywordsHYDROLASE / DPP9 / Protease
Function / homology
Function and homology information


dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding ...dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding / nucleus / cytosol
Similarity search - Function
Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / 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
Similarity search - Domain/homology
PHOSPHATE ION / Dipeptidyl peptidase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRoss, B.H. / Huber, R.
CitationJournal: To Be Published
Title: Discovery and Development of 4-Oxo-beta-Lactams as Novel Inhibitors of Dipeptidyl Peptidases 8 and 9
Authors: Fehr, L. / Carvalho, L.A.R. / Ross, B.H. / Lum, K. / Vieira, A.C. / Kiefersauer, R. / Geiss-Friedlander, R. / Kaiser, M. / Rodrigues, T. / Lucas, S.D. / Cravatt, B.F. / Huber, R. / Moreira, R.
History
DepositionAug 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
B: Dipeptidyl peptidase 9
A: Dipeptidyl peptidase 9
C: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)411,07310
Polymers410,5094
Non-polymers5646
Water2,324129
1
B: Dipeptidyl peptidase 9
A: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,6286
Polymers205,2542
Non-polymers3744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-31 kcal/mol
Surface area63800 Å2
MethodPISA
2
C: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,4444
Polymers205,2542
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-31 kcal/mol
Surface area63760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.170, 95.310, 127.196
Angle α, β, γ (deg.)86.560, 102.540, 102.440
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Dipeptidyl peptidase 9 / / DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / ...DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / Dipeptidyl peptidase-like protein 9 / DPLP9


Mass: 102627.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP9, DPRP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86TI2, dipeptidyl-peptidase IV
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.08 M Na-Cacodilate pH 5.25, 0.16 M Ca-Acetate, 30 % Glycerol, 10 % PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→46.89 Å / Num. obs: 92941 / % possible obs: 98.4 % / Redundancy: 2.235 % / Biso Wilson estimate: 50.051 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.115 / Χ2: 0.946 / Net I/σ(I): 7.24 / Num. measured all: 207713 / Scaling rejects: 330
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-2.972.2990.4912.0615790700268690.8060.64598.1
2.97-3.062.2840.3962.515304682267000.8510.52198.2
3.06-3.152.2660.3083.0315214683367150.910.40698.3
3.15-3.252.2360.2673.3815230692168100.9270.35198.4
3.25-3.372.2190.2164.0214900683067140.9450.28598.3
3.37-3.512.1240.1574.9714047673766120.9670.20898.1
3.51-3.672.0810.1195.9113896683266780.9780.15897.7
3.67-3.872.1450.1036.8214265675866500.9810.13698.4
3.87-4.122.3590.0838.5715851683567190.9880.1198.3
4.12-4.452.3180.06210.5715252664965800.9910.08399
4.45-4.92.3070.05711.4315255669866130.990.07698.7
4.9-5.632.2590.06210.6514882665765890.990.08299
5.63-6.872.1130.06210.2812074577657150.9890.08298.9
6.87-8.72.1790.04314.337751362235570.9930.05798.2
8.7-11.182.3660.0320.124280183418090.9970.0498.6
11.18-16.312.3460.0321.562616113711150.9950.0498.1
16.31-26.12.2620.02321.188803983890.9980.03197.7
26.1-46.892.1120.0222.32261301070.9990.02682.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EOR

6eor


Resolution: 2.9→46.89 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.87 / SU B: 25.629 / SU ML: 0.448 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29 4647 5 %RANDOM
Rwork0.223 ---
obs0.2264 88289 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.73 Å2 / Biso mean: 59.125 Å2 / Biso min: 9.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å2-5.08 Å25.61 Å2
2---0.99 Å2-5.08 Å2
3---2.13 Å2
Refinement stepCycle: final / Resolution: 2.9→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25524 0 32 129 25685
Biso mean--80.43 30.88 -
Num. residues----3155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01326315
X-RAY DIFFRACTIONr_bond_other_d0.0010.01723620
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.64335712
X-RAY DIFFRACTIONr_angle_other_deg1.0611.56954952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40353121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.80522.2941421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.669154266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.71515143
X-RAY DIFFRACTIONr_chiral_restr0.0450.23228
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0229226
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025759
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 343 -
Rwork0.395 6523 -
all-6866 -
obs--98.07 %

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