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- PDB-6i56: Crystal structure of PBSX exported protein XepA -

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Basic information

Entry
Database: PDB / ID: 6i56
TitleCrystal structure of PBSX exported protein XepA
ComponentsPhage-like element PBSX protein XepA
KeywordsUNKNOWN FUNCTION / XepA / PBSX exported protein / XkdY / P31
Function / homologyPhage-like element PBSX protein XepA
Function and homology information
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsHakansson, M. / Svensson, L.A. / Welin, M. / Al-Karadaghi, S.
Funding support1items
OrganizationGrant numberCountry
European Union685778
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS.
Authors: Freitag-Pohl, S. / Jasilionis, A. / Hakansson, M. / Svensson, L.A. / Kovacic, R. / Welin, M. / Watzlawick, H. / Wang, L. / Altenbuchner, J. / Plotka, M. / Kaczorowska, A.K. / Kaczorowski, T. ...Authors: Freitag-Pohl, S. / Jasilionis, A. / Hakansson, M. / Svensson, L.A. / Kovacic, R. / Welin, M. / Watzlawick, H. / Wang, L. / Altenbuchner, J. / Plotka, M. / Kaczorowska, A.K. / Kaczorowski, T. / Nordberg Karlsson, E. / Al-Karadaghi, S. / Walse, B. / Aevarsson, A. / Pohl, E.
History
DepositionNov 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2May 15, 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
D: Phage-like element PBSX protein XepA
A: Phage-like element PBSX protein XepA
C: Phage-like element PBSX protein XepA
B: Phage-like element PBSX protein XepA
E: Phage-like element PBSX protein XepA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,44311
Polymers151,8915
Non-polymers5536
Water15,511861
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42430 Å2
ΔGint-186 kcal/mol
Surface area50320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.810, 106.467, 158.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22C
13D
23B
14D
24E
15A
25C
16A
26B
17A
27E
18C
28B
19C
29E
110B
210E

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
11TYRTYRVALVALDA4 - 2784 - 278
21TYRTYRVALVALAB4 - 2784 - 278
12TYRTYRVALVALDA4 - 2784 - 278
22TYRTYRVALVALCC4 - 2784 - 278
13TYRTYRVALVALDA4 - 2784 - 278
23TYRTYRVALVALBD4 - 2784 - 278
14TYRTYRVALVALDA4 - 2784 - 278
24TYRTYRVALVALEE4 - 2784 - 278
15VALVALVALVALAB2 - 2782 - 278
25VALVALVALVALCC2 - 2782 - 278
16LYSLYSVALVALAB3 - 2783 - 278
26LYSLYSVALVALBD3 - 2783 - 278
17LYSLYSVALVALAB3 - 2783 - 278
27LYSLYSVALVALEE3 - 2783 - 278
18LYSLYSVALVALCC3 - 2783 - 278
28LYSLYSVALVALBD3 - 2783 - 278
19LYSLYSVALVALCC3 - 2783 - 278
29LYSLYSVALVALEE3 - 2783 - 278
110LYSLYSSERSERBD3 - 2793 - 279
210LYSLYSSERSEREE3 - 2793 - 279

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Phage-like element PBSX protein XepA / Protein XkdY


Mass: 30378.119 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Gene: xepA, xkdY, BSU12780 / Cell line (production host): pHWG1186 E.coli JM109 / Production host: Escherichia coli (E. coli) / References: UniProt: P39797
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium acetate pH 5.0, 6 % (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97954 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2.12→29.86 Å / Num. obs: 83224 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.049 / Rrim(I) all: 0.156 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.12-2.1610.22.0721.245340.5130.6762.181100
11.02-29.848.60.0356600.9990.0130.03895.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.3data scaling
PDB_EXTRACT3.24data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.12→29.86 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.46 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.182
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 4107 4.9 %RANDOM
Rwork0.1726 ---
obs0.175 79037 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.32 Å2 / Biso mean: 47.701 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2.12→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10642 0 36 861 11539
Biso mean--72.07 48.51 -
Num. residues----1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01310936
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710121
X-RAY DIFFRACTIONr_angle_refined_deg1.681.63814815
X-RAY DIFFRACTIONr_angle_other_deg1.3761.57823431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.66451394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24923.202534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.427151810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0141552
X-RAY DIFFRACTIONr_chiral_restr0.0730.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022324
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D79450.09
12A79450.09
21D79460.09
22C79460.09
31D79860.08
32B79860.08
41D79680.09
42E79680.09
51A80240.08
52C80240.08
61A80370.08
62B80370.08
71A80310.08
72E80310.08
81C80540.08
82B80540.08
91C80520.09
92E80520.09
101B81100.09
102E81100.09
LS refinement shellResolution: 2.12→2.175 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 285 -
Rwork0.298 5815 -
all-6100 -
obs--100 %
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)
11.2141-0.7264-0.59242.02231.0961.840.06430.4346-0.1759-0.2693-0.14370.17760.0846-0.13530.07940.0795-0.0028-0.02840.3494-0.04310.031417.687-4.917-49.048
22.5614-0.42750.24272.67540.77483.5324-0.06960.00610.2322-0.01270.057-0.0471-0.10140.29940.01250.0456-0.0159-0.00440.22710.04020.049539.001-47.215-0.361
33.1282-0.9717-0.47110.91180.12680.18620.0760.20280.1138-0.2182-0.0628-0.1084-0.00020.0787-0.01310.0658-0.00390.02720.23040.00010.013638.0330.998-40.385
43.03350.31920.04882.46950.83483.166-0.0266-0.07970.15540.00780.02070.0109-0.2189-0.00210.00580.13160.00260.00090.1593-0.00630.067627.561-33.5518.297
53.19890.78330.30281.08070.3151.03950.01660.26830.0312-0.1081-0.03160.2221-0.088-0.12720.0150.0180.025-0.02350.24050.01410.05861.4214.98-36.252
62.5407-0.1453-0.1862.03310.15472.9030.00740.09390.01410.0387-0.00690.06680.1377-0.0419-0.00060.0539-0.00360.01380.23220.01350.008520.411-57.844-14.716
71.52830.35060.99851.13921.10672.60010.05970.15340.1749-0.070.0742-0.1397-0.15020.3048-0.1340.0214-0.00310.03150.21620.00810.059434.31214.677-22.326
83.487-0.18320.33121.8057-0.00853.1258-0.1251-0.07740.05520.02490.1110.0624-0.5175-0.35550.0140.16820.10420.02530.26760.02460.08421.993-35.2115.174
92.4185-0.8155-1.15860.9170.87422.15180.14420.04870.3281-0.0433-0.04570.0032-0.2154-0.0205-0.09850.0272-0.0060.02310.15710.02080.067911.70217.115-19.754
103.02760.2108-0.09472.96551.10073.0585-0.02420.180.0194-0.1410.00080.122-0.0414-0.32940.02330.0081-0.0077-0.00320.36220.00840.0807-2.503-50.18-5.416
110.05220.5937-0.35277.1466-4.26052.54530.0250.0089-0.00220.09980.10030.2303-0.0224-0.0591-0.12530.28580.00160.0120.385-0.03270.257118.498-16.902-17.217
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 144
2X-RAY DIFFRACTION2A172 - 279
3X-RAY DIFFRACTION3B3 - 144
4X-RAY DIFFRACTION4B172 - 279
5X-RAY DIFFRACTION5C2 - 144
6X-RAY DIFFRACTION6C172 - 279
7X-RAY DIFFRACTION7D4 - 144
8X-RAY DIFFRACTION8D172 - 279
9X-RAY DIFFRACTION9E3 - 144
10X-RAY DIFFRACTION10E172 - 279
11X-RAY DIFFRACTION11A145 - 171
12X-RAY DIFFRACTION11B145 - 171
13X-RAY DIFFRACTION11C145 - 171
14X-RAY DIFFRACTION11D145 - 171
15X-RAY DIFFRACTION11E145 - 171

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