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- PDB-6eom: Structure of DPP III from Caldithrix abyssi -

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Basic information

Entry
Database: PDB / ID: 6eom
TitleStructure of DPP III from Caldithrix abyssi
ComponentsMutT/NUDIX family protein
KeywordsHYDROLASE / Caldithrix abyssi / Metallopeptidase / Dipeptidyl peptidase III / DPP III / Zinc-Hydrolase
Function / homologyPeptidase family M49 / Peptidase family M49 / dipeptidyl-peptidase activity / Prokaryotic membrane lipoprotein lipid attachment site profile. / metal ion binding / cytoplasm / ALANINE / LYSINE / MutT/NUDIX family protein
Function and homology information
Biological speciesCaldithrix abyssi DSM 13497 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsSabljic, I.
Funding support Croatia, 1items
OrganizationGrant numberCountry
Croatian Science Foundation7235 Croatia
CitationJournal: PLoS ONE / Year: 2018
Title: The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity.
Authors: Sabljic, I. / Tomin, M. / Matovina, M. / Sucec, I. / Tomasic Paic, A. / Tomic, A. / Abramic, M. / Tomic, S.
History
DepositionOct 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MutT/NUDIX family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9958
Polymers65,5111
Non-polymers4847
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-56 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.472, 90.549, 132.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MutT/NUDIX family protein / Peptidase family M49


Mass: 65511.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldithrix abyssi DSM 13497 (bacteria) / Gene: Cabys_2252, Calab_3349 / Plasmid: pET-21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H1XW48

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Non-polymers , 7 types, 342 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#6: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH 6.5, 25% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2705 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: 1.2705 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 36965 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 29.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.042 / Rrim(I) all: 0.124 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.168.30.81929540.9030.2980.87398.4
8.92-47.998.20.0375680.9990.0140.0499.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.17data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se-Met labeled protein solved using MAD metode

Resolution: 2.103→48 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.42
RfactorNum. reflection% reflection
Rfree0.2398 1858 5.04 %
Rwork0.2097 --
obs0.2113 36872 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.93 Å2 / Biso mean: 38.3051 Å2 / Biso min: 19.87 Å2
Refinement stepCycle: final / Resolution: 2.103→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 26 335 4584
Biso mean--44.19 41.01 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034386
X-RAY DIFFRACTIONf_angle_d0.4485911
X-RAY DIFFRACTIONf_chiral_restr0.039632
X-RAY DIFFRACTIONf_plane_restr0.004774
X-RAY DIFFRACTIONf_dihedral_angle_d15.792660
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1025-2.15940.35281490.29482602275198
2.1594-2.22290.31871300.272126502780100
2.2229-2.29470.35831580.27126432801100
2.2947-2.37670.27711320.249726892821100
2.3767-2.47180.31061430.256626462789100
2.4718-2.58430.27381330.247926912824100
2.5843-2.72050.2961440.242826682812100
2.7205-2.8910.26661170.238426942811100
2.891-3.11420.29061330.234327012834100
3.1142-3.42750.27381650.214926912856100
3.4275-3.92320.24591220.185427382860100
3.9232-4.94210.15761550.15727342889100
4.9421-48.01380.18041770.17828673044100
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)
10.74170.36110.13941.51980.49281.307-0.01970.0197-0.0309-0.12070.003-0.06590.02350.02120.01340.27130.00120.05550.22350.05270.37454.69515.8159-33.5787
20.4273-1.18131.28713.2256-3.53253.8057-0.0330.03090.16730.1194-0.1916-0.4549-0.11430.30410.17850.2315-0.03080.00630.28270.00210.42058.48713.2078-12.0325
33.0007-1.42130.0471.8887-0.15220.85230.01870.0690.1658-0.01210.01350.0304-0.0275-0.1083-0.03420.2052-0.03110.02750.2630.04290.3072-4.656-9.2353-6.526
46.66765.3244-2.44274.2765-2.15622.5937-0.40070.098-0.043-0.51720.2461-0.21580.2403-0.0290.15960.270.03490.05740.30270.01980.3604-8.777114.5112-24.524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 32:250))A32 - 250
2X-RAY DIFFRACTION2chain 'A' and ((resseq 251:342))A251 - 342
3X-RAY DIFFRACTION3chain 'A' and ((resseq 343:540))A343 - 540
4X-RAY DIFFRACTION4chain 'A' and ((resseq 541:555))A541 - 555

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