[English] 日本語
Yorodumi
- PDB-6fij: Structure of the loading/condensing region (SAT-KS-MAT) of the ce... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fij
TitleStructure of the loading/condensing region (SAT-KS-MAT) of the cercosporin fungal non-reducing polyketide synthase (NR-PKS) CTB1
ComponentsPolyketide synthase
KeywordsBIOSYNTHETIC PROTEIN / NR-PKS / PKS / iPKS / iterative PKS / non-reducing / SAT / starter acyl / condensing / loading / polyketide / fungal
Function / homology
Function and homology information


secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process
Similarity search - Function
Polyketide product template domain / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Polyketide synthase, thioesterase domain / Thioesterase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / CurL-like, PKS C-terminal / Thioesterase / Thioesterase domain ...Polyketide product template domain / Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Polyketide synthase, thioesterase domain / Thioesterase / Starter unit:ACP transacylase / Starter unit:ACP transacylase in aflatoxin biosynthesis / CurL-like, PKS C-terminal / Thioesterase / Thioesterase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / 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 / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Non-reducing polyketide synthase CTB1
Similarity search - Component
Biological speciesCercospora nicotianae (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsHerbst, D.A. / Jakob, R.P. / Townsend, C.A. / Maier, T.
Funding support Switzerland, United States, 5items
OrganizationGrant numberCountry
Swiss National Science Foundation159696 Switzerland
Swiss National Science Foundation145023 Switzerland
Swiss National Science Foundation164074 Switzerland
Swiss National Science Foundation138262 Switzerland
National Institutes of HealthES001670 United States
CitationJournal: Nat Chem Biol / Year: 2018
Title: The structural organization of substrate loading in iterative polyketide synthases.
Authors: Dominik A Herbst / Callie R Huitt-Roehl / Roman P Jakob / Jacob M Kravetz / Philip A Storm / Jamie R Alley / Craig A Townsend / Timm Maier /
Abstract: Polyketide synthases (PKSs) are microbial multienzymes for the biosynthesis of biologically potent secondary metabolites. Polyketide production is initiated by the loading of a starter unit onto an ...Polyketide synthases (PKSs) are microbial multienzymes for the biosynthesis of biologically potent secondary metabolites. Polyketide production is initiated by the loading of a starter unit onto an integral acyl carrier protein (ACP) and its subsequent transfer to the ketosynthase (KS). Initial substrate loading is achieved either by multidomain loading modules or by the integration of designated loading domains, such as starter unit acyltransferases (SAT), whose structural integration into PKS remains unresolved. A crystal structure of the loading/condensing region of the nonreducing PKS CTB1 demonstrates the ordered insertion of a pseudodimeric SAT into the condensing region, which is aided by the SAT-KS linker. Cryo-electron microscopy of the post-loading state trapped by mechanism-based crosslinking of ACP to KS reveals asymmetry across the CTB1 loading/-condensing region, in accord with preferential 1:2 binding stoichiometry. These results are critical for re-engineering the loading step in polyketide biosynthesis and support functional relevance of asymmetric conformations of PKSs.
History
DepositionJan 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Refinement description
Category: citation / refine / Item: _citation.year / _refine.details
Revision 1.2Apr 11, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_abbrev ..._chem_comp.name / _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyketide synthase
B: Polyketide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,71418
Polymers280,6062
Non-polymers1,10816
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration, cryoEM, structure homology (all PKS are dimers)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17530 Å2
ΔGint-28 kcal/mol
Surface area89630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.050, 230.200, 253.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1407-

MG

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Polyketide synthase


Mass: 140303.062 Da / Num. of mol.: 2 / Mutation: T321A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cercospora nicotianae (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6DQW3

-
Non-polymers , 5 types, 368 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.81 Å3/Da / Density % sol: 56.32 % / Description: plate-like
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M MgCl2 0.1 M Bis-Tris Propane pH 6.5 18% (v/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→126.915 Å / Num. obs: 79860 / % possible obs: 99.2 % / Redundancy: 8.5 % / Biso Wilson estimate: 60.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.212 / Net I/σ(I): 10.13
Reflection shellResolution: 2.77→2.84 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.938 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 5448 / CC1/2: 0.433 / % possible all: 91.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HG4, 4RO5

2hg4

4ro5


Resolution: 2.77→63.45 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1 / Stereochemistry target values: ML
Details: UNIDENTIFIED DIFFERENCE DENSITY AROUND THE ACTIVE SITE RESIDUES C553 AND C119, POSSIBLY DUE TO PARTIAL ACYLATION OR OXIDATION. THE DIFFERENCE DENSITY IN THE REGION AROUND RESIDUES 651 TO 661 ...Details: UNIDENTIFIED DIFFERENCE DENSITY AROUND THE ACTIVE SITE RESIDUES C553 AND C119, POSSIBLY DUE TO PARTIAL ACYLATION OR OXIDATION. THE DIFFERENCE DENSITY IN THE REGION AROUND RESIDUES 651 TO 661 INDICATES MULTIPLE DIFFERENT MAIN CHAIN CONFORMATION, WHEREAS ONLY ONE COULD ME MODELLED. BASED ON OBSERVED B-FACTORS AND THE FACT THAT CRYSTALLIZATION WAS CARRIED OUT IN THE PRESENCE OF 0.3M MG(2+) SOME SURFACE WATERS MIGHT ALSO REPRESENT PARTIALLY OCCUPIED HYDRATED MAGNESIUM IONS.
RfactorNum. reflection% reflection
Rfree0.2405 3916 4.91 %
Rwork0.2052 --
obs0.2069 79812 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.77→63.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19291 0 69 352 19712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219940
X-RAY DIFFRACTIONf_angle_d0.49627153
X-RAY DIFFRACTIONf_dihedral_angle_d11.92512022
X-RAY DIFFRACTIONf_chiral_restr0.043085
X-RAY DIFFRACTIONf_plane_restr0.0033570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7698-2.80360.45421320.46262366X-RAY DIFFRACTION89
2.8036-2.83910.43971270.40512551X-RAY DIFFRACTION93
2.8391-2.87640.37671250.36732608X-RAY DIFFRACTION96
2.8764-2.91580.3661290.35362699X-RAY DIFFRACTION99
2.9158-2.95750.3861250.3222707X-RAY DIFFRACTION99
2.9575-3.00160.30451430.30392673X-RAY DIFFRACTION100
3.0016-3.04850.32491400.28642698X-RAY DIFFRACTION100
3.0485-3.09850.33331410.28472742X-RAY DIFFRACTION100
3.0985-3.15190.32091420.27572694X-RAY DIFFRACTION100
3.1519-3.20920.35121440.2692705X-RAY DIFFRACTION100
3.2092-3.2710.30811420.2582721X-RAY DIFFRACTION100
3.271-3.33770.30091400.25382688X-RAY DIFFRACTION100
3.3377-3.41030.28561220.24452721X-RAY DIFFRACTION100
3.4103-3.48960.25521450.22822754X-RAY DIFFRACTION100
3.4896-3.57690.2351450.21492686X-RAY DIFFRACTION100
3.5769-3.67360.23821530.21192714X-RAY DIFFRACTION100
3.6736-3.78170.23971540.19032719X-RAY DIFFRACTION100
3.7817-3.90370.19931310.19352732X-RAY DIFFRACTION100
3.9037-4.04320.22721370.17792732X-RAY DIFFRACTION100
4.0432-4.20510.20671450.17492731X-RAY DIFFRACTION100
4.2051-4.39640.23641540.15492730X-RAY DIFFRACTION100
4.3964-4.62810.18141380.15292746X-RAY DIFFRACTION100
4.6281-4.9180.17181490.1492756X-RAY DIFFRACTION100
4.918-5.29750.17761350.162761X-RAY DIFFRACTION100
5.2975-5.83030.21561500.17562749X-RAY DIFFRACTION100
5.8303-6.67320.21071440.18422796X-RAY DIFFRACTION100
6.6732-8.40440.20031360.16752814X-RAY DIFFRACTION100
8.4044-63.46660.23091480.192903X-RAY DIFFRACTION99
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)
10.23050.05160.0682.5314-0.80640.57560.0381-0.05390.13420.0927-0.01260.3934-0.0409-0.027-0.04280.5078-0.11810.00210.5741-0.08190.5185-6.268185.6464-22.2192
21.76550.82840.22152.66640.35661.35160.2133-0.27880.37460.4609-0.16840.1906-0.11410.1333-0.04770.4688-0.10590.02190.4324-0.00980.3535-2.719548.3417-7.6392
32.38190.61641.20240.54220.19841.14190.1742-0.28660.05550.0945-0.12310.24640.1814-0.2935-0.04940.4609-0.0506-0.01340.43890.01290.5061-43.376426.2176-29.1474
42.05591.01960.6411.98460.93592.2877-0.07810.08110.2811-0.00720.0838-0.0026-0.29880.2446-0.01790.4555-0.0457-0.16650.44180.03830.6883-33.083158.356-50.3213
51.25510.34040.34191.09770.17740.90350.02470.1637-0.0968-0.1140.0233-0.05450.08470.0276-0.05890.3357-0.0063-0.02950.4102-0.00720.268710.873646.3087-35.6
60.48190.25440.13243.00080.25710.1008-0.04420.09520.10290.20350.0265-0.6904-0.1190.20670.01270.5035-0.0987-0.09890.59180.06820.575734.380991.4807-25.4051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 441 )
2X-RAY DIFFRACTION2chain 'A' and (resid 442 through 805 )
3X-RAY DIFFRACTION3chain 'A' and (resid 806 through 1288 )
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 337 )
5X-RAY DIFFRACTION5chain 'B' and (resid 338 through 823 )
6X-RAY DIFFRACTION6chain 'B' and (resid 824 through 1288 )

+
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