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- PDB-5sdm: PanDDA analysis group deposition -- Crystal Structure of Porphyro... -

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Basic information

Entry
Database: PDB / ID: 5sdm
TitlePanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z1328078283
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
Chem-I8A / Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.039 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)162,0347
Polymers161,5072
Non-polymers5275
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.009, 117.089, 147.927
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-I8A / N-(cyclopropylmethyl)-2,2,3,3-tetramethylazetidine-1-carboxamide


Mass: 210.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H22N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
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 2M / Detector: PIXEL / Date: Aug 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 2.043→67.939 Å / Num. obs: 105328 / % possible obs: 96.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 41.3 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.036 / Rrim(I) all: 0.093 / Net I/σ(I): 11.5 / Num. measured all: 687460
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.043-2.1155.42831852680.6040.5261.211.359.2
5.766-67.9396.53423852650.9960.0220.05529.799.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5jwf


Resolution: 2.039→67.94 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.873 / SU R Cruickshank DPI: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 5351 5.08 %RANDOM
Rwork0.228 ---
obs0.2293 105339 93.9 %-
Displacement parametersBiso max: 120.53 Å2 / Biso mean: 40.98 Å2 / Biso min: 20.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.4709 Å20 Å20 Å2
2--0.6469 Å20 Å2
3----0.1761 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.039→67.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10951 0 33 266 11250
Biso mean--67.89 41.55 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3884SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1938HARMONIC5
X-RAY DIFFRACTIONt_it11232HARMONIC10
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_contact9021SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11232HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg15224HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion17.1
LS refinement shellResolution: 2.04→2.09 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2131 116 5.51 %
Rwork0.1972 1991 -
all-2107 -
obs--28.29 %
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)
10.6452-0.14940.21230.4243-0.07560.55670.0278-0.2472-0.06560.00830.0784-0.0206-0.0042-0.107-0.1062-0.08690.0454-0.02350.0018-0.0112-0.095413.308122.305542.4306
20.2207-0.0550.11120.4069-0.00930.4605-0.07140.02120.0146-0.05220.05-0.01140.01640.01310.0214-0.04490.00680.0026-0.0495-0.0257-0.04573.33811.1048-6.1536
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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