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

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Basic information

Entry
Database: PDB / ID: 5sdp
TitlePanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z2277255954
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-I8J / Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.195 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

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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)162,0527
Polymers161,5072
Non-polymers5455
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.111, 117.236, 147.926
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-I8J / 5-fluoro-1-(1-methylcyclopropane-1-sulfonyl)-1,2,3,6-tetrahydropyridine


Mass: 219.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14FNO2S / 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.: 228 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
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 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 2.195→84.034 Å / Num. obs: 66330 / % possible obs: 92.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 50.23 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Net I/σ(I): 12.7 / Num. measured all: 448097
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.195-2.40572320133170.610.5321.4131.567.6
6.785-84.0346.32096933160.9990.0160.03936.999.8

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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: 2.195→84.03 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.37 / SU Rfree Blow DPI: 0.243 / SU Rfree Cruickshank DPI: 0.248
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 3381 5.1 %RANDOM
Rwork0.2155 ---
obs0.2171 66330 72.7 %-
Displacement parametersBiso max: 97.8 Å2 / Biso mean: 47.09 Å2 / Biso min: 20.53 Å2
Baniso -1Baniso -2Baniso -3
1-2.228 Å20 Å20 Å2
2--0.5381 Å20 Å2
3----2.7661 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.195→84.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10951 0 31 228 11210
Biso mean--48.37 41.06 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3897SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1941HARMONIC5
X-RAY DIFFRACTIONt_it11252HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1430SEMIHARMONIC5
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_d11252HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg15251HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion18.01
LS refinement shellResolution: 2.19→2.35 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2776 74 5.58 %
Rwork0.2221 1253 -
all-1327 -
obs--8.24 %
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)
10.7571-0.12230.35810.6241-0.12810.70530.1095-0.25610.0104-0.09020.0709-0.00240.0403-0.1254-0.1805-0.0641-0.0011-0.01220.0069-0.0113-0.154413.600422.128842.4897
20.4085-0.16270.19580.5094-0.14450.9047-0.08610.0573-0.0126-0.1140.09270.0197-0.1587-0.0106-0.00660.0112-0.0212-0.0137-0.0822-0.0058-0.11423.310911.1478-6.0089
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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