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

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Basic information

Entry
Database: PDB / ID: 5sdk
TitlePanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z416341642
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-I87 / Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.977 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)162,0867
Polymers161,5072
Non-polymers5795
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.588, 117.512, 147.913
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-I87 / (2S)-N,2-dimethyl-N-(propan-2-yl)morpholine-4-sulfonamide


Mass: 236.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20N2O3S / 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.: 265 / 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: 2.73 Å3/Da / Density % sol: 55 %
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: 1.99→92.009 Å / Num. obs: 91010 / % possible obs: 95.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 43.26 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Net I/σ(I): 16 / Num. measured all: 609216
Reflection shell

Num. unique all: 4551 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.99-2.1476.2282250.6520.4621.1851.775.4
6.087-92.0096.52943810.0110.02750.199.8

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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: 1.977→92.01 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.235 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.23 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.183
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 4620 5.08 %RANDOM
Rwork0.2178 ---
obs0.2189 91013 73.4 %-
Displacement parametersBiso max: 142.3 Å2 / Biso mean: 44.48 Å2 / Biso min: 23.68 Å2
Baniso -1Baniso -2Baniso -3
1-3.8064 Å20 Å20 Å2
2---0.2526 Å20 Å2
3----3.5538 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 1.977→92.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10951 0 33 265 11249
Biso mean--113.88 43.88 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3880SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1934HARMONIC5
X-RAY DIFFRACTIONt_it11230HARMONIC10
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_contact9111SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11230HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg15216HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion16.61
LS refinement shellResolution: 1.98→2.08 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2188 107 5.88 %
Rwork0.2075 1714 -
all-1821 -
obs--10.38 %
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)
10.5186-0.06460.08910.3929-0.03860.38590.0644-0.1676-0.02330.0030.0293-0.00050.0067-0.0469-0.09370.00470.0382-0.0124-0.0251-0.0205-0.148313.436922.185342.5487
20.3635-0.14670.08180.3247-0.07720.5271-0.07690.0551-0.0159-0.0630.05820.0035-0.0492-0.01690.01870.0227-0.005-0.0024-0.0756-0.0151-0.11673.329611.1534-6.0399
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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