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- PDB-5na6: Structure of Cys-null Se-Met DPP III from Bacteroides thetaiotaomicron -

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Basic information

Entry
Database: PDB / ID: 5na6
TitleStructure of Cys-null Se-Met DPP III from Bacteroides thetaiotaomicron
ComponentsPutative dipeptidyl-peptidase III
KeywordsHYDROLASE / Bacteroides thetaiotaomicron / Metallopeptidase / Dipeptidyl peptidase III / Zinc-Hydrolase / Cys-null
Function / homologyPeptidase family M49 / Peptidase family M49 / dipeptidyl-peptidase activity / metal ion binding / cytoplasm / ACETATE ION / Chem-PE3 / Dipeptidyl-peptidase III
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSabljic, I. / Luic, M.
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structure of dipeptidyl peptidase III from the human gut symbiont Bacteroides thetaiotaomicron.
Authors: Sabljic, I. / Mestrovic, N. / Vukelic, B. / Macheroux, P. / Gruber, K. / Luic, M. / Abramic, M.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative dipeptidyl-peptidase III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7699
Polymers77,6881
Non-polymers1,0818
Water10,359575
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-51 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.442, 103.442, 141.225
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1159-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative dipeptidyl-peptidase III


Mass: 77687.539 Da / Num. of mol.: 1 / Mutation: C11S, C158S, C189S, C425S, C450S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Gene: BT_1846 / Plasmid: pET-21b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8A6N1, dipeptidyl-peptidase III

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Non-polymers , 6 types, 583 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H58O15
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium acetate, 0.1 M MES pH 6.5, 30% glycerol ethoxylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 3, 2014
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.9→48.57 Å / Num. obs: 69127 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.035 / Rrim(I) all: 0.094 / Net I/σ(I): 15.7 / Num. measured all: 479085 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.946.70.7240.8460.2970.78496.6
9.11-48.576.40.0460.9990.0190.0599.2

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
160.9666.6859.627S201
239.51817.34727.342S200.987
338.8284.44135.604S200.945
470.99319.82113.076S200.88
574.87218.2859.415S200.878
673.912.84116.067S200.87
752.2622.52712.986S200.869
839.1819.240.035S200.835
933.85111.35441.678S200.741
1054.78424.14137.958S200.483
1129.49912.91417.15S200.289
1270.41122.8426.612S200.18
1362.10330.95110.13S200.179
14100.8140.794.363S200.167
1582.46826.80826.703S200.157
1638.8285.57439.62S200.154
1759.11425.1258.282S200.139
1841.74128.70638.724S200.129
1961.08610.44510.128S200.08
2033.58115.28225.477S200.078
2184.92325.78930.165S200.041

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Processing

Software
NameVersionClassification
XDSdata reduction
SHELXphasing
SHELXDphasing
Aimless0.5.17data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.9→48.566 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.86
RfactorNum. reflection% reflection
Rfree0.2001 3331 4.82 %
Rwork0.1731 --
obs0.1744 69078 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.01 Å2 / Biso mean: 31.2482 Å2 / Biso min: 14.35 Å2
Refinement stepCycle: final / Resolution: 1.9→48.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 69 575 5758
Biso mean--50.88 38.31 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085333
X-RAY DIFFRACTIONf_angle_d0.8697230
X-RAY DIFFRACTIONf_chiral_restr0.056784
X-RAY DIFFRACTIONf_plane_restr0.005942
X-RAY DIFFRACTIONf_dihedral_angle_d14.0643162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.92730.33651290.28372585271495
1.9273-1.95610.311300.239426942824100
1.9561-1.98660.26311580.227127122870100
1.9866-2.01920.2881240.207326872811100
2.0192-2.0540.23631270.197827232850100
2.054-2.09140.24971480.192226962844100
2.0914-2.13160.19361350.184927252860100
2.1316-2.17510.21591400.184627182858100
2.1751-2.22240.211090.182727262835100
2.2224-2.27410.20541560.171627302886100
2.2741-2.3310.231310.184627312862100
2.331-2.3940.23151210.179727472868100
2.394-2.46440.19121270.173527662893100
2.4644-2.5440.21611310.186627132844100
2.544-2.63490.2531370.184127562893100
2.6349-2.74040.21641450.183627302875100
2.7404-2.86510.23711710.18427192890100
2.8651-3.01610.24881500.182627402890100
3.0161-3.2050.22131330.184827672900100
3.205-3.45240.19831230.171127912914100
3.4524-3.79970.18371600.158227642924100
3.7997-4.34930.13221410.135627702911100
4.3493-5.47840.14581550.143428222977100
5.4784-48.58230.17661500.166929353085100
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)
10.65450.1345-0.72120.11180.01950.9355-0.11910.06280.2131-0.1134-0.00980.2026-0.2138-0.34660.1290.27070.0035-0.08230.2718-0.04610.320830.88075.69789.8952
21.9569-0.52010.02551.18850.11191.15430.07710.0520.0426-0.0472-0.05540.0899-0.0852-0.0503-0.01780.1724-0.00470.01480.20420.01060.169129.94449.478330.4271
31.52320.92060.67531.30290.80971.0762-0.31250.09250.3049-0.38410.10450.197-0.30520.01890.06410.3707-0.0955-0.07260.10350.05670.238956.277814.25193.1776
41.59940.43970.16390.7220.09040.2415-0.1110.2216-0.2059-0.22550.1046-0.0807-0.09030.13850.01440.2651-0.08410.00680.1457-0.0050.206558.9482-0.15184.5665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 329 through 414)A329 - 414
2X-RAY DIFFRACTION2chain 'A' and (resid 415 through 623)A415 - 623
3X-RAY DIFFRACTION3chain 'A' and (resid 24 through 328 )A24 - 328
4X-RAY DIFFRACTION4chain 'A' and (resid 624 through 675 )A624 - 675

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