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- PDB-6fwy: Thioester domain of the Enterococcus faecium TIE86 protein -

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Basic information

Entry
Database: PDB / ID: 6fwy
TitleThioester domain of the Enterococcus faecium TIE86 protein
ComponentsB-type Cna protein
KeywordsUNKNOWN FUNCTION / LPXTG-anchored / surface protein / thioester domain / TIE protein
Function / homologyThioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / B-type Cna protein
Function and homology information
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsMiller, O.K. / Banfield, M.J. / Schwarz-Linek, U.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K001485 United Kingdom
Royal Society of Edinburgh United Kingdom
Citation
Journal: Protein Sci. / Year: 2018
Title: A new structural class of bacterial thioester domains reveals a slipknot topology.
Authors: Miller, O.K. / Banfield, M.J. / Schwarz-Linek, U.
#1: Journal: Elife / Year: 2015
Title: An internal thioester in a pathogen surface protein mediates covalent host binding.
Authors: Walden, M. / Edwards, J.M. / Dziewulska, A.M. / Bergmann, R. / Saalbach, G. / Kan, S.Y. / Miller, O.K. / Weckener, M. / Jackson, R.J. / Shirran, S.L. / Botting, C.H. / Florence, G.J. / ...Authors: Walden, M. / Edwards, J.M. / Dziewulska, A.M. / Bergmann, R. / Saalbach, G. / Kan, S.Y. / Miller, O.K. / Weckener, M. / Jackson, R.J. / Shirran, S.L. / Botting, C.H. / Florence, G.J. / Rohde, M. / Banfield, M.J. / Schwarz-Linek, U.
History
DepositionMar 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_data_processing_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Revision 1.3May 8, 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_asym_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_asym_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: B-type Cna protein
B: B-type Cna protein
C: B-type Cna protein
D: B-type Cna protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,7586
Polymers121,4724
Non-polymers2862
Water6,017334
1
A: B-type Cna protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5622
Polymers30,3681
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: B-type Cna protein


Theoretical massNumber of molelcules
Total (without water)30,3681
Polymers30,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: B-type Cna protein


Theoretical massNumber of molelcules
Total (without water)30,3681
Polymers30,3681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: B-type Cna protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4602
Polymers30,3681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.700, 33.732, 206.052
Angle α, β, γ (deg.)90.000, 105.880, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYALAALAAA1 - 2801 - 280
21GLYGLYALAALABB1 - 2801 - 280
12ALAALAARGARGAA2 - 2792 - 279
22ALAALAARGARGCC2 - 2792 - 279
13ALAALAARGARGAA2 - 2792 - 279
23ALAALAARGARGDD2 - 2792 - 279
14ALAALAARGARGBB2 - 2792 - 279
24ALAALAARGARGCC2 - 2792 - 279
15ALAALAARGARGBB2 - 2792 - 279
25ALAALAARGARGDD2 - 2792 - 279
16ALAALAALAALACC2 - 2802 - 280
26ALAALAALAALADD2 - 2802 - 280

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
B-type Cna protein


Mass: 30367.916 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: B4W81_16995, BTA13_08335, DTPHA_1402599 / Plasmid: pEHisTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1A7T0E1
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: sodium citrate, ammonium sulfate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.14→198.2 Å / Num. obs: 69192 / % possible obs: 93.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 41.45 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.9
Reflection shellResolution: 2.14→2.18 Å / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.6 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.24data extraction
xia2data reduction
xia2data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→198.19 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.912 / SU B: 18.289 / SU ML: 0.22 / SU R Cruickshank DPI: 0.2835 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.212
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 3399 4.9 %RANDOM
Rwork0.2333 ---
obs0.2345 65791 93.66 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 72.82 Å2 / Biso mean: 41.448 Å2 / Biso min: 26.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å2-0.1 Å2
2---4.28 Å20 Å2
3---2.25 Å2
Refinement stepCycle: final / Resolution: 2.14→198.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8536 0 19 334 8889
Biso mean--44.97 40.8 -
Num. residues----1118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.028829
X-RAY DIFFRACTIONr_bond_other_d0.0060.027969
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.93611944
X-RAY DIFFRACTIONr_angle_other_deg0.863318639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8951132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55824.738344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.914151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.9571520
X-RAY DIFFRACTIONr_chiral_restr0.0750.21306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219825
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021775
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A177800.06
12B177800.06
21A175540.06
22C175540.06
31A175380.07
32D175380.07
41B176800.05
42C176800.05
51B176280.06
52D176280.06
61C176660.06
62D176660.06
LS refinement shellResolution: 2.141→2.197 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 244 -
Rwork0.323 5038 -
all-5282 -
obs--98.4 %
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)
10.8945-0.48220.45311.6799-1.27872.6891-0.02070.0039-0.01510.1069-0.0273-0.1921-0.11960.04860.04790.4401-0.0087-0.06790.3461-0.00720.041-29.6736-0.304214.4389
27.9793-4.67395.99745.411-4.00026.04910.19210.1970.1325-0.1287-0.2091-0.44560.15490.43690.0170.3892-0.005-0.02560.39870.05530.3068-4.0613-29.523738.7741
32.5089-2.41512.1322.7362-2.12451.8251-0.0217-0.05270.00470.1169-0.018-0.2249-0.0173-0.03260.03970.50630.0062-0.1150.40990.0240.1265-14.9664-25.64238.5926
41.20140.3239-0.02491.7468-1.37762.8827-0.10740.0406-0.0073-0.24430.0026-0.15910.1918-0.00250.10470.6252-0.0221-0.01090.3507-0.02020.0184-62.9074-19.883880.1433
51.14431.8538-1.68354.8323-3.17583.6655-0.10780.0747-0.0018-0.3714-0.0476-0.22170.14080.18050.15540.566-0.01240.03010.4550.07570.1993-49.44818.613348.9007
62.30682.7257-2.84614.4179-4.04494.05130.00640.01180.14090.06160.0057-0.2475-0.00910.0188-0.01210.5554-0.0225-0.02390.4064-0.01650.1858-61.1821-0.652363.4389
72.00391.0341-0.71233.3855-1.13761.8423-0.02260.0958-0.08820.0147-0.06310.1080.0185-0.1080.08570.36920.0187-0.01570.3582-0.01570.0332-63.15253.950817.8805
81.21171.49690.07046.298-2.78743.30090.1288-0.0488-0.06960.47510.0440.1779-0.0231-0.2468-0.17280.488-0.06310.02360.4532-0.01610.2229-79.6984-24.599450.284
90.41340.7034-0.60973.2171-3.37614.69510.0111-0.0672-0.0535-0.14640.09560.1040.3636-0.1997-0.10680.4763-0.0375-0.0120.444-0.05180.1865-75.8838-16.890732.2949
102.6562-1.53250.84393.5061-0.76391.1471-0.0986-0.10860.13010.04290.02930.11180.0104-0.14060.06940.5371-0.0326-0.05560.37680.03080.0342.8813-7.823586.5707
112.8701-3.48183.51324.5314-4.51844.5917-0.1230.02960.11780.03530.0066-0.0141-0.0544-0.11150.11640.59450.0136-0.10750.380.0070.1959-4.878312.002966.2273
121.2328-1.65261.94232.6936-3.04533.6826-0.101-0.0975-0.01010.3560.22930.2452-0.2865-0.2958-0.12820.61960.0459-0.0670.44240.0260.2442-18.660118.143267.0032
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 156
2X-RAY DIFFRACTION2A157 - 171
3X-RAY DIFFRACTION3A172 - 280
4X-RAY DIFFRACTION4B2 - 151
5X-RAY DIFFRACTION5B152 - 242
6X-RAY DIFFRACTION6B243 - 280
7X-RAY DIFFRACTION7C2 - 156
8X-RAY DIFFRACTION8C157 - 230
9X-RAY DIFFRACTION9C231 - 280
10X-RAY DIFFRACTION10D2 - 142
11X-RAY DIFFRACTION11D143 - 171
12X-RAY DIFFRACTION12D172 - 280

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