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Basic information

Entry
Database: PDB / ID: 5sdl
TitlePanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z321318226
ComponentsAsp/Glu-specific dipeptidyl-peptidase
KeywordsHYDROLASE / Diamond I04-1 fragment screening / PanDDA / XChemExplorer / peptidase / Porphyromonas gingivalis
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
N-(4-methoxyphenyl)-N'-pyridin-4-ylurea / Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.44 Å
AuthorsTham, C.T. / Coker, J.A. / Krojer, T. / Foster, W.R. / Koekemoer, L. / Douangamath, A. / Talon, R. / Fearon, D. / von Delft, F. / Yue, W.W. ...Tham, C.T. / Coker, J.A. / Krojer, T. / Foster, W.R. / Koekemoer, L. / Douangamath, A. / Talon, R. / Fearon, D. / von Delft, F. / Yue, W.W. / Bountra, C. / Bezerra, G.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
University of Oxford0006369 United Kingdom
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Tham, C.T. / Coker, J.A. / Krojer, T. / Foster, W.R. / Koekemoer, L. / Douangamath, A. / Talon, R. / Fearon, D. / von Delft, F. / Yue, W.W. / Bountra, C. / Bezerra, G.A.
History
DepositionJan 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Asp/Glu-specific dipeptidyl-peptidase
B: Asp/Glu-specific dipeptidyl-peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,0646
Polymers161,5072
Non-polymers5574
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.920, 117.470, 147.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Asp/Glu-specific dipeptidyl-peptidase / Dipeptidyl-peptidase 11 / DPP11


Mass: 80753.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: dpp11, PGN_0607 / Production host: Escherichia coli (E. coli)
References: UniProt: B2RID1, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Chemical ChemComp-JHJ / N-(4-methoxyphenyl)-N'-pyridin-4-ylurea


Mass: 243.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.09 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: Morpheus Buffer system 1, 0.06M Divalents, 30% v/v Precipitant Mix 3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 2.44→59.82 Å / Num. obs: 66710 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 76.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Net I/σ(I): 14.2 / Num. measured all: 445964 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.44-2.571.6513405748850.5770.6721.7831.1100
10.91-59.8260.02551968590.9970.0120.02848.399.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (18-SEP-2020)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5JWF

5jwf


Resolution: 2.44→59.82 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.367 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.362 / SU Rfree Blow DPI: 0.235 / SU Rfree Cruickshank DPI: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 3377 5.07 %RANDOM
Rwork0.2094 ---
obs0.2109 66638 100 %-
Displacement parametersBiso max: 128.81 Å2 / Biso mean: 68.1 Å2 / Biso min: 43.14 Å2
Baniso -1Baniso -2Baniso -3
1--11.7567 Å20 Å20 Å2
2---0.6059 Å20 Å2
3---12.3625 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.44→59.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10951 0 38 258 11247
Biso mean--123.81 65.8 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3872SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1940HARMONIC5
X-RAY DIFFRACTIONt_it11238HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1428SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8934SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11238HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg15220HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion17.77
LS refinement shellResolution: 2.44→2.46 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.264 71 5.33 %
Rwork0.2394 1262 -
all-1333 -
obs--99.93 %
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)
10.7269-0.17350.26160.6665-0.12910.72350.1201-0.2127-0.0119-0.0730.0540.01660.0508-0.0969-0.1742-0.10280.0174-0.0307-0.0286-0.0141-0.147613.487822.251742.5081
20.5622-0.34590.10060.5805-0.09920.8527-0.0984-0.01580.0403-0.05590.0549-0.0303-0.18450.04230.0435-0.0327-0.0184-0.0014-0.0657-0.0187-0.07933.313111.2566-6.199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A22 - 720
2X-RAY DIFFRACTION2{ B|* }B23 - 720

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