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- PDB-5sds: PanDDA analysis group deposition of ground-state model of Porphyr... -

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Basic information

Entry
Database: PDB / ID: 5sds
TitlePanDDA analysis group deposition of ground-state model of Porphyromonas gingivalis DPP11
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
Asp/Glu-specific dipeptidyl-peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.91 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 of ground-state model
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

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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)161,6135
Polymers161,5072
Non-polymers1063
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.773, 117.328, 147.556
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-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
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: 54.9 %
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: 1.907→91.835 Å / Num. obs: 101212 / % possible obs: 96.2 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 15.6 / Num. measured all: 670359
Reflection shell

Num. unique all: 5061 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.907-2.0745.7289212820.670.4451.0941.680.8
5.863-91.8356.53281410.0120.034799.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimlessdata scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5JWF

5jwf


Resolution: 1.91→91.835 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.957 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 5185 5.1 %RANDOM
Rwork0.2131 ---
obs0.2148 96027 73.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.24 Å2 / Biso mean: 37.635 Å2 / Biso min: 20.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20 Å2
2---0.04 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.91→91.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10951 0 3 266 11220
Biso mean--58.52 40.45 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311200
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710155
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.64715172
X-RAY DIFFRACTIONr_angle_other_deg1.3651.58223446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.24451388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.32221.851632
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.705151840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0291586
X-RAY DIFFRACTIONr_chiral_restr0.0730.21428
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022500
X-RAY DIFFRACTIONr_mcbond_it2.9363.9285564
X-RAY DIFFRACTIONr_mcbond_other2.9363.9285563
X-RAY DIFFRACTIONr_mcangle_it4.1635.8846948
LS refinement shellResolution: 1.907→1.957 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 9 -
Rwork0.312 282 -
all-291 -
obs--2.88 %

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