[English] 日本語
Yorodumi
- PDB-6i56: Crystal structure of PBSX exported protein XepA -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more