[English] 日本語
Yorodumi
- PDB-8h6s: Structure of acyltransferase VinK in complex with the loading acy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8h6s
TitleStructure of acyltransferase VinK in complex with the loading acyl carrier protein of vicenistatin PKS
Components
  • Malonyl-CoA-[acyl-carrier-protein] transacylase
  • Polyketide synthase modules 1-3
KeywordsTRANSFERASE / acyl carrier protein / polyketide synthase / acyltransferase
Function / homology
Function and homology information


[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 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 / zinc ion binding ...[acyl-carrier-protein] S-malonyltransferase / [acyl-carrier-protein] S-malonyltransferase activity / 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 / zinc ion binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / VinK acyltransferase small domain / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Zinc-binding dehydrogenase / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain ...: / VinK acyltransferase small domain / Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / : / Polyketide synthase extender module SpnB, Rossmann fold domain / Zinc-binding dehydrogenase / : / 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. / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, enoylreductase domain / Enoylreductase / 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 / GroES-like superfamily / 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
Similarity search - Domain/homology
Chem-9EF / Polyketide synthase modules 1-3 / [acyl-carrier-protein] S-malonyltransferase
Similarity search - Component
Biological speciesStreptomyces halstedii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKawada, K. / Miyanaga, A. / Chisuga, T. / Kudo, F. / Eguchi, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H02911 Japan
Japan Society for the Promotion of Science (JSPS)17K07747 Japan
CitationJournal: Biochemistry / Year: 2023
Title: Structural Basis of Transient Interactions of Acyltransferase VinK with the Loading Acyl Carrier Protein of the Vicenistatin Modular Polyketide Synthase.
Authors: Miyanaga, A. / Kawada, K. / Chisuga, T. / Kudo, F. / Eguchi, T.
History
DepositionOct 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Malonyl-CoA-[acyl-carrier-protein] transacylase
B: Malonyl-CoA-[acyl-carrier-protein] transacylase
C: Polyketide synthase modules 1-3
D: Polyketide synthase modules 1-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5818
Polymers105,7664
Non-polymers8154
Water21612
1
A: Malonyl-CoA-[acyl-carrier-protein] transacylase
C: Polyketide synthase modules 1-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2914
Polymers52,8832
Non-polymers4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Malonyl-CoA-[acyl-carrier-protein] transacylase
D: Polyketide synthase modules 1-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2914
Polymers52,8832
Non-polymers4082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.363, 90.626, 113.511
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
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A19 - 317
2010B19 - 317
1020C13 - 106
2020D13 - 106

NCS ensembles :
ID
1
2

-
Components

#1: Protein Malonyl-CoA-[acyl-carrier-protein] transacylase


Mass: 38170.211 Da / Num. of mol.: 2 / Mutation: S106C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinK / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY5
#2: Protein Polyketide synthase modules 1-3


Mass: 14712.665 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinP1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-9EF / N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 383.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity % sol: 35.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, magnesium chloride, Tris-HCl, and D-glucose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2019
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16764 / % possible obs: 99.9 % / Redundancy: 5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.173 / Net I/σ(I): 9.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.992 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2385 / CC1/2: 0.735 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZD

5czd


Resolution: 3→46.01 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 27.672 / SU ML: 0.462 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 814 4.9 %RANDOM
Rwork0.21 ---
obs0.2129 15908 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.81 Å2 / Biso mean: 64.029 Å2 / Biso min: 23.03 Å2
Baniso -1Baniso -2Baniso -3
1-6.81 Å20 Å20 Å2
2---5.91 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 3→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6051 0 50 12 6113
Biso mean--73.35 36.81 -
Num. residues----781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136231
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175839
X-RAY DIFFRACTIONr_angle_refined_deg1.351.6558463
X-RAY DIFFRACTIONr_angle_other_deg1.7481.5813419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3065775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.04220.171351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26515977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6991565
X-RAY DIFFRACTIONr_chiral_restr0.050.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021405
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A90210.06
12B90210.06
21C28700.08
22D28700.08
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 40 -
Rwork0.342 1159 -
all-1199 -
obs--100 %

+
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