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- PDB-3dkt: Crystal structure of Thermotoga maritima encapsulin -

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Basic information

Entry
Database: PDB / ID: 3dkt
TitleCrystal structure of Thermotoga maritima encapsulin
Components
  • Maritimacin
  • Putative uncharacterized protein
KeywordsSTRUCTURAL PROTEIN/VIRUS LIKE PARTICLE / enzyme encapsulation / nanocompartment / oxidative stress / ferritin-like protein / hk97-fold / Antibiotic / Antimicrobial / Bacteriocin / Cobalt / Hydrolase / Protease / Secreted / STRUCTURAL PROTEIN-VIRUS LIKE PARTICLE COMPLEX
Function / homology
Function and homology information


encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / iron ion transport / intracellular iron ion homeostasis / proteolysis
Similarity search - Function
Major capsid protein gp5 fold - #30 / hypothetical protein PF0899 domain / Major capsid protein gp5 fold / Ferritin-like protein / hypothetical protein PF0899 fold / Type 1 encapsulin shell protein / Encapsulating protein for peroxidase / Ferritin-like / Ferritin-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type 1 encapsulin shell protein / Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.104 Å
AuthorsSutter, M. / Boehringer, D. / Gutmann, S. / Weber-Ban, E. / Ban, N.
CitationJournal: Nat Struct Mol Biol / Year: 2008
Title: Structural basis of enzyme encapsulation into a bacterial nanocompartment.
Authors: Markus Sutter / Daniel Boehringer / Sascha Gutmann / Susanne Günther / David Prangishvili / Martin J Loessner / Karl O Stetter / Eilika Weber-Ban / Nenad Ban /
Abstract: Compartmentalization is an important organizational feature of life. It occurs at varying levels of complexity ranging from eukaryotic organelles and the bacterial microcompartments, to the molecular ...Compartmentalization is an important organizational feature of life. It occurs at varying levels of complexity ranging from eukaryotic organelles and the bacterial microcompartments, to the molecular reaction chambers formed by enzyme assemblies. The structural basis of enzyme encapsulation in molecular compartments is poorly understood. Here we show, using X-ray crystallographic, biochemical and EM experiments, that a widespread family of conserved bacterial proteins, the linocin-like proteins, form large assemblies that function as a minimal compartment to package enzymes. We refer to this shell-forming protein as 'encapsulin'. The crystal structure of such a particle from Thermotoga maritima determined at 3.1-angstroms resolution reveals that 60 copies of the monomer assemble into a thin, icosahedral shell with a diameter of 240 angstroms. The interior of this nanocompartment is lined with conserved binding sites for short polypeptide tags present as C-terminal extensions of enzymes involved in oxidative-stress response.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Aug 31, 2011Group: Database references / Source and taxonomy
Revision 1.4Nov 6, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.5Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maritimacin
B: Maritimacin
C: Maritimacin
D: Maritimacin
E: Maritimacin
F: Maritimacin
G: Maritimacin
H: Maritimacin
I: Maritimacin
J: Maritimacin
K: Putative uncharacterized protein
L: Putative uncharacterized protein
M: Putative uncharacterized protein
N: Putative uncharacterized protein
O: Putative uncharacterized protein
P: Putative uncharacterized protein
Q: Putative uncharacterized protein
R: Putative uncharacterized protein
S: Putative uncharacterized protein
T: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)313,33720
Polymers313,33720
Non-polymers00
Water1,802100
1
A: Maritimacin
B: Maritimacin
C: Maritimacin
D: Maritimacin
E: Maritimacin
F: Maritimacin
G: Maritimacin
H: Maritimacin
I: Maritimacin
J: Maritimacin
K: Putative uncharacterized protein
L: Putative uncharacterized protein
M: Putative uncharacterized protein
N: Putative uncharacterized protein
O: Putative uncharacterized protein
P: Putative uncharacterized protein
Q: Putative uncharacterized protein
R: Putative uncharacterized protein
S: Putative uncharacterized protein
T: Putative uncharacterized protein
x 6


Theoretical massNumber of molelcules
Total (without water)1,880,024120
Polymers1,880,024120
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_555-y+1/4,-x+1/4,-z+1/41
crystal symmetry operation19_555-x+1/4,-z+1/4,-y+1/41
crystal symmetry operation24_555-z+1/4,-y+1/4,-x+1/41
Unit cell
Length a, b, c (Å)669.040, 669.040, 669.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11J
21A
31B
41C
51D
61E
71F
81G
91H
101I

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 4 - 267 / Label seq-ID: 1 - 264

Dom-IDAuth asym-IDLabel asym-ID
1JJ
2AA
3BB
4CC
5DD
6EE
7FF
8GG
9HH
10II

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Components

#1: Protein
Maritimacin / Thermotoga bacteriocin


Mass: 30516.787 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Thermotoga maritima (bacteria) / Strain: MSB8, DSM3109
References: UniProt: Q9WZP2, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein/peptide
Putative uncharacterized protein / Ferritin-like protein


Mass: 816.948 Da / Num. of mol.: 10
Fragment: C-terminal encapsulin binding peptide, UNP residues 106-113'
Source method: isolated from a natural source / Source: (natural) Thermotoga maritima (bacteria) / Strain: MSB8, DSM3109 / References: UniProt: Q9WZP3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 9.89 Å3/Da / Density % sol: 87.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 0.1M citrate, 21.5% MPD (v/v), 0.25M ammonium acetate, pH5.1, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0008 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0008 Å / Relative weight: 1
ReflectionResolution: 3.1→49.867 Å / Num. all: 228096 / Num. obs: 220152 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 8.63 % / Biso Wilson estimate: 73.242 Å2 / Rmerge(I) obs: 0.265 / Net I/σ(I): 7.43
Reflection shellResolution: 3.1→3.3 Å / Redundancy: 8.89 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 331841 / Num. unique all: 37311 / Num. unique obs: 37311 / % possible all: 96.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata scaling
AVE/DMphasing
RefinementResolution: 3.104→49.867 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.756 / SU ML: 0.55 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.239 10961 5 %RANDOM
Rwork0.219 ---
obs0.22 219258 96.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.455 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso max: 283.8 Å2 / Biso mean: 128.241 Å2 / Biso min: 51.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.775 Å2-0 Å2-0 Å2
2---1.775 Å2-0 Å2
3----1.775 Å2
Refinement stepCycle: LAST / Resolution: 3.104→49.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21970 0 0 100 22070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922370
X-RAY DIFFRACTIONf_angle_d1.3330150
X-RAY DIFFRACTIONf_chiral_restr0.0783330
X-RAY DIFFRACTIONf_plane_restr0.0053890
X-RAY DIFFRACTIONf_dihedral_angle_d20.2188470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11J2207X-RAY DIFFRACTIONPOSITIONAL
12A2207X-RAY DIFFRACTIONPOSITIONAL0.041
13B2207X-RAY DIFFRACTIONPOSITIONAL0.045
14C2207X-RAY DIFFRACTIONPOSITIONAL0.041
15D2207X-RAY DIFFRACTIONPOSITIONAL0.044
16E2207X-RAY DIFFRACTIONPOSITIONAL0.046
17F2207X-RAY DIFFRACTIONPOSITIONAL0.043
18G2207X-RAY DIFFRACTIONPOSITIONAL0.043
19H2207X-RAY DIFFRACTIONPOSITIONAL0.042
110I2207X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
3.104-3.1390.4233440.41665606904656092
3.139-3.1760.4523740.415713375077133100
3.176-3.2150.433720.414706674387066100
3.215-3.2560.4013750.407711174867111100
3.256-3.2990.383730.395709574687095100
3.299-3.3440.4143760.389713275087132100
3.344-3.3920.4043740.384711174857111100
3.392-3.4420.3923330.37863516684635193
3.442-3.4960.382650.37450535318505388
3.496-3.5530.3933740.348710974837109100
3.553-3.6150.3613750.333712474997124100
3.615-3.680.3543130.32959126225591295
3.68-3.7510.3193340.31263626696636293
3.751-3.8280.3193760.281716275387162100
3.828-3.9110.293040.26757456049574595
3.911-4.0020.263460.25265736919657395
4.002-4.1020.2453760.222714675227146100
4.102-4.2130.2263780.197718775657187100
4.213-4.3370.2173780.187717275507172100
4.337-4.4760.2163780.178719175697191100
4.476-4.6360.1893770.166716375407163100
4.636-4.8220.1733790.161719875777198100
4.822-5.0410.1613790.151720775867207100
5.041-5.3060.1823800.155721075907210100
5.306-5.6390.1983820.169725176337251100
5.639-6.0730.1873820.164727176537271100
6.073-6.6830.2113830.173727976627279100
6.683-7.6470.1743870.153734377307343100
7.647-9.6230.1283900.118741778077417100
9.623-49.8740.2054040.276638067766399
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)
10.81310.1985-0.7109-0.1115-0.31840.0126-0.18930.19290.1496-0.24820.2062-0.0517-0.17270.10990.00011.2054-0.5724-0.09481.16110.06770.6939127.3097138.660512.1352
20.10730.19580.09290.6629-0.6416-0.2013-0.14210.23030.3074-0.11120.07720.1763-0.17620.0810.00011.317-0.4811-0.28841.06130.14040.715388.3824137.827-0.7233
3-0.2215-0.04330.34290.1826-0.73930.741-0.20010.1559-0.0436-0.29830.11830.2553-0.19920.140.00011.1084-0.4237-0.15121.1149-0.00460.642880.9573100.1931-15.1133
4-0.2229-0.18940.4086-0.41690.38460.9017-0.0050.2529-0.1277-0.20460.1122-0.1032-0.05660.300401.0129-0.44650.07241.2686-0.19710.653115.360977.8042-11.2787
5-0.2299-0.198-0.3845-0.30550.53340.1355-0.05490.3351-0.07140.06060.1902-0.1814-0.0240.28-00.9944-0.52180.11491.4241-0.1780.7606144.0246101.5615.5211
60.21640.49440.76890.14230.36970.48390.1635-0.0508-0.3117-0.02020.1164-0.03990.27690.0206-0.00010.7935-0.0462-0.1340.615-0.33940.740364.624-1.534635.9492
70.66260.4916-0.0080.68970.5923-0.47190.07430.0633-0.18810.05760.0352-0.15240.02420.22110.00010.90060.0983-0.23090.8786-0.45230.9383105.4002-3.153939.2753
80.1161-0.4668-0.24830.4918-0.0023-0.1289-0.00610.2147-0.0719-0.03310.0415-0.1743-0.12980.195500.8385-0.074-0.03771.1273-0.56260.859121.314924.128312.7909
90.8862-0.5135-0.5013-0.30350.20230.46960.0240.23420.1198-0.21880.0532-0.0661-0.02980.17860.00010.878-0.2333-0.04250.9888-0.38740.688990.262442.4067-6.9615
10-0.36060.479-0.1947-0.18760.13791.3369-0.0870.243-0.1147-0.04070.2166-0.00530.1254-0.1116-00.7565-0.1153-0.10820.6707-0.29870.680655.2926.6067.4696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J

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