[English] 日本語
Yorodumi
- PDB-5eny: Ketosynthase from module 6 connected to acyl carrier protein from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eny
TitleKetosynthase from module 6 connected to acyl carrier protein from module 5 (unobservable) of the bacillaene synthase from Bacillus subtilis 168
ComponentsPolyketide synthase PksL
KeywordsHYDROLASE / trans-AT ketosynthase / polyketide / bacillaene
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / fatty acid biosynthetic process / oxidoreductase activity / cytoplasm
Similarity search - Function
: / RhiE-like, KS-MAT linker domain / Prismane-like superfamily / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch ...: / RhiE-like, KS-MAT linker domain / Prismane-like superfamily / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase, dehydratase domain superfamily / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / : / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyketide synthase PksL
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4 Å
AuthorsWagner, D.T. / Gay, D.C. / Keatinge-Clay, A.T.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: The LINKS motif zippers trans-acyltransferase polyketide synthase assembly lines into a biosynthetic megacomplex.
Authors: Gay, D.C. / Wagner, D.T. / Meinke, J.L. / Zogzas, C.E. / Gay, G.R. / Keatinge-Clay, A.T.
History
DepositionNov 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
A: Polyketide synthase PksL
B: Polyketide synthase PksL
C: Polyketide synthase PksL
D: Polyketide synthase PksL
E: Polyketide synthase PksL
F: Polyketide synthase PksL
G: Polyketide synthase PksL
H: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)686,5608
Polymers686,5608
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17380 Å2
ΔGint-83 kcal/mol
Surface area165580 Å2
2
A: Polyketide synthase PksL
B: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)171,6402
Polymers171,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-19 kcal/mol
Surface area42210 Å2
MethodPISA
3
C: Polyketide synthase PksL
D: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)171,6402
Polymers171,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-19 kcal/mol
Surface area42050 Å2
MethodPISA
4
E: Polyketide synthase PksL
F: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)171,6402
Polymers171,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-19 kcal/mol
Surface area42100 Å2
MethodPISA
5
G: Polyketide synthase PksL
H: Polyketide synthase PksL


Theoretical massNumber of molelcules
Total (without water)171,6402
Polymers171,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-19 kcal/mol
Surface area42090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.106, 112.732, 211.441
Angle α, β, γ (deg.)104.96, 90.07, 106.32
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 3 - 591 / Label seq-ID: 176 - 764

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16AA
26GG
17AA
27HH
18BB
28CC
19BB
29DD
110BB
210EE
111BB
211FF
112BB
212GG
113BB
213HH
114CC
214DD
115CC
215EE
116CC
216FF
117CC
217GG
118CC
218HH
119DD
219EE
120DD
220FF
121DD
221GG
122DD
222HH
123EE
223FF
124EE
224GG
125EE
225HH
126FF
226GG
127FF
227HH
128GG
228HH

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

-
Components

#1: Protein
Polyketide synthase PksL / PKS


Mass: 85819.969 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: pksL, outG, pksA, pksX, BSU17190 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05470
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25 mg/ml PksACP5+KS6, 150 mM NaCl, 10% glycerol, 10 mM HEPES, pH 7.5) with 1 uL crystallization buffer (30% PEG 4000 (v/v), 0.2 M sodium acetate, 0.1 M Tris, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→39.77 Å / Num. obs: 23712 / % possible obs: 98.7 % / Redundancy: 3.3 % / Net I/σ(I): 6.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 4→39.77 Å / Cor.coef. Fo:Fc: 0.822 / Cor.coef. Fo:Fc free: 0.797 / Cross valid method: THROUGHOUT / ESU R Free: 1.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.354 2126 5.1 %RANDOM
Rwork0.33349 ---
obs0.33451 -92.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 154.659 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.03 Å20.02 Å2
2---0.18 Å2-0.05 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 4→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34416 0 0 0 34416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01935180
X-RAY DIFFRACTIONr_bond_other_d00.0233136
X-RAY DIFFRACTIONr_angle_refined_deg0.8521.96147576
X-RAY DIFFRACTIONr_angle_other_deg3.58376484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97554340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72724.4911612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.181156020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.26715172
X-RAY DIFFRACTIONr_chiral_restr0.0680.25148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02139700
X-RAY DIFFRACTIONr_gen_planes_other0.0050.027864
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.16315.38217492
X-RAY DIFFRACTIONr_mcbond_other8.16315.38217491
X-RAY DIFFRACTIONr_mcangle_it12.0323.04521788
X-RAY DIFFRACTIONr_mcangle_other12.0323.04621789
X-RAY DIFFRACTIONr_scbond_it7.47615.85617688
X-RAY DIFFRACTIONr_scbond_other7.47615.85617689
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.01123.61725789
X-RAY DIFFRACTIONr_long_range_B_refined17.9338919
X-RAY DIFFRACTIONr_long_range_B_other17.92938920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A629860.15
12B629860.15
21A702780.12
22C702780.12
31A630360.16
32D630360.16
41A700220.13
42E700220.13
51A630780.16
52F630780.16
61A700000.12
62G700000.12
71A642860.12
72H642860.12
81B630920.15
82C630920.15
91B659980.11
92D659980.11
101B634100.15
102E634100.15
111B655580.12
112F655580.12
121B640700.12
122G640700.12
131B654360.13
132H654360.13
141C633540.15
142D633540.15
151C703160.12
152E703160.12
161C640620.13
162F640620.13
171C701260.12
172G701260.12
181C632560.15
182H632560.15
191D642420.12
192E642420.12
201D660520.12
202F660520.12
211D634660.15
212G634660.15
221D656460.13
222H656460.13
231E633040.15
232F633040.15
241E708900.1
242G708900.1
251E633060.16
252H633060.16
261F630340.15
262G630340.15
271F656020.12
272H656020.12
281G632760.16
282H632760.16
LS refinement shellResolution: 4.004→4.107 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 129 -
Rwork0.383 2247 -
obs--71.54 %

+
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