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- PDB-5olj: Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4 -

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Basic information

Entry
Database: PDB / ID: 5olj
TitleCrystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4
ComponentsDipeptidyl peptidase IV
KeywordsHYDROLASE / dipeptidyl peptidase 4 / peptidase inhibitor / Porphyromonas gingivalis / biofilm / dipeptidyl peptidase 9
Function / homology
Function and homology information


serine-type peptidase activity / proteolysis
Similarity search - Function
: / 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 / Alpha Beta
Similarity search - Domain/homology
Dipeptidyl peptidase IV
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFulop, V.
Funding support Belgium, 4items
OrganizationGrant numberCountry
Fund for Scientific Research (FWO-Flanders)G.0173.09N Belgium
Agency for Innovation by Science and Technology in Flanders (IWT, Belgium)SBO 50164 Belgium
Industrial Research Fund of the University of LeuvenIOF/KP/09/003 Belgium
European Union223077 (NEUROPRO) Belgium
Citation
Journal: Eur J Med Chem / Year: 2017
Title: Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4 and structure-activity relationships based on inhibitor profiling.
Authors: Rea, D. / Van Elzen, R. / De Winter, H. / Van Goethem, S. / Landuyt, B. / Luyten, W. / Schoofs, L. / Van Der Veken, P. / Augustyns, K. / De Meester, I. / Fulop, V. / Lambeir, A.M.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2004
Title: Expression, purification and preliminary crystallographic analysis of dipeptidyl peptidase IV from Porphyromonas gingivalis.
Authors: Rea, D. / Lambeir, A.M. / Kumagai, Y. / De Meester, I. / Scharpe, S. / Fulop, V.
History
DepositionJul 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 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

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Assembly

Deposited unit
A: Dipeptidyl peptidase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1802
Polymers82,0881
Non-polymers921
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint1 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.100, 109.100, 157.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1101-

HOH

21A-1170-

HOH

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Components

#1: Protein Dipeptidyl peptidase IV


Mass: 82087.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: dppIV, PGN_1469 / Production host: Porphyromonas gingivalis (bacteria) / References: UniProt: B2RKU3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 290 K / Method: vapor diffusion
Details: 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.02 M sodium L-glutamate, 0.02 M DL-alanine, 0.02 M glycine, 0.02 M DL-lysine, 0.02 M DLserine, and 0.1 M BICINE/TRIS pH 8.5
PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→38 Å / Num. obs: 48811 / % possible obs: 99.7 % / Redundancy: 9.3 % / Net I/σ(I): 10.8

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KBY

5kby


Resolution: 2.2→37.87 Å / Cor.coef. Fo:Fc: 0.839 / Cor.coef. Fo:Fc free: 0.81 / SU B: 9.784 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25451 1974 4 %RANDOM
Rwork0.22379 ---
obs0.22502 46837 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.429 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0 Å2
2---0.75 Å20 Å2
3---1.5 Å2
Refinement stepCycle: 1 / Resolution: 2.2→37.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5631 0 6 398 6035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195774
X-RAY DIFFRACTIONr_bond_other_d0.0010.025334
X-RAY DIFFRACTIONr_angle_refined_deg1.6341.9427826
X-RAY DIFFRACTIONr_angle_other_deg0.812312236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1545702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53623.38284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06115948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1021542
X-RAY DIFFRACTIONr_chiral_restr0.0940.2834
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026608
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021422
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.531 137 -
Rwork0.529 3288 -
obs--96.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.111-3.56232.89723.0108-1.86133.7690.14370.6439-0.0122-0.0539-0.08320.0101-0.30740.2134-0.06040.0749-0.03420.0210.1115-0.0210.00949.696237.199216.0372
21.40821.9872-0.84394.47390.00651.36770.0798-0.0116-0.0667-0.0004-0.0781-0.1508-0.1127-0.0493-0.00170.0539-0.0309-0.01630.04570.00640.017525.193343.37972.3556
30.26530.10420.00760.2512-0.04490.3427-0.033-0.00230.0395-0.0361-0.00180.0503-0.0395-0.06240.03480.05320.0094-0.01350.0368-0.01250.028219.292458.113422.9238
40.28740.11780.10270.23560.08510.28980.01010.0131-0.01570.03220.0085-0.00340.04130.0066-0.01860.0625-0.0004-0.01730.0304-0.00980.009536.368335.093832.7516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 43
2X-RAY DIFFRACTION2A44 - 80
3X-RAY DIFFRACTION3A81 - 321
4X-RAY DIFFRACTION4A322 - 723

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