[English] 日本語
Yorodumi
- PDB-9iyw: Crystal structure of chimeric KSQ-AT didomain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9iyw
TitleCrystal structure of chimeric KSQ-AT didomain
ComponentsPolyketide synthase,GfsA KSQ-AncAT chimeric protein
KeywordsTRANSFERASE / Polyketide biosynthesis / Decarboxylase / Acyltransferase / Thiolase fold
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / secondary metabolite biosynthetic process / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / antibiotic biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / lyase activity
Similarity search - Function
Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / : ...Polyketide synthase dimerisation element domain / Polyketide synthase dimerisation element domain / : / Polyketide synthase dehydratase N-terminal domain / Polyketide synthase, dehydratase domain / PKS_DH / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / Polyketide synthase, dehydratase domain superfamily / 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 / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / 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
Similarity search - Domain/homology
Polyketide synthase GfsA
Similarity search - Component
Biological speciesStreptomyces graminofaciens (bacteria)
synthetic construt (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChisuga, T. / Miyanaga, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H02911 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Ancestral sequence reconstruction as a tool for structural analysis of modular polyketide synthases
Authors: Chisuga, T. / Takinami, S. / Liao, Z. / Karasawa, M. / Adachi, N. / Kawasaki, M. / Moriya, T. / Senda, T. / Terada, T. / Kudo, F. / Eguchi, T. / Nakano, S. / Ito, S. / Miyanaga, A.
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyketide synthase,GfsA KSQ-AncAT chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1552
Polymers96,1321
Non-polymers231
Water3,189177
1
A: Polyketide synthase,GfsA KSQ-AncAT chimeric protein
hetero molecules

A: Polyketide synthase,GfsA KSQ-AncAT chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,3104
Polymers192,2642
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5550 Å2
ΔGint-53 kcal/mol
Surface area58460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.065, 76.065, 352.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1272-

HOH

-
Components

#1: Protein Polyketide synthase,GfsA KSQ-AncAT chimeric protein


Mass: 96131.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The original sequence region (Gly559-Arg870) of GfsA (Uniprot: E0D202) was substituted with the artificial sequence.
Source: (gene. exp.) Streptomyces graminofaciens (bacteria), (gene. exp.) synthetic construt (others)
Gene: gfsA / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E0D202
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: SOKALAN PA 25 CL

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 24, 2023
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: 2→50 Å / Num. obs: 81441 / % possible obs: 99.9 % / Redundancy: 7.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.4
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4265 / CC1/2: 0.774 / % possible all: 98

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.21 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 12.176 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24612 4063 5 %RANDOM
Rwork0.20144 ---
obs0.20361 77202 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.595 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.7 Å20 Å2
2--1.39 Å20 Å2
3----4.52 Å2
Refinement stepCycle: 1 / Resolution: 2→48.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6182 0 1 177 6360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136319
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175942
X-RAY DIFFRACTIONr_angle_refined_deg1.941.6328596
X-RAY DIFFRACTIONr_angle_other_deg1.4561.5713636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6135827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20319.673336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.01815927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0171568
X-RAY DIFFRACTIONr_chiral_restr0.0910.2799
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027302
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021446
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_it3.4924.8433332
X-RAY DIFFRACTIONr_mcbond_other3.4924.8423331
X-RAY DIFFRACTIONr_mcangle_it4.7367.2414151
X-RAY DIFFRACTIONr_mcangle_other4.7367.2424152
X-RAY DIFFRACTIONr_scbond_it4.025.2582987
X-RAY DIFFRACTIONr_scbond_other4.0225.2562985
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7957.7364445
X-RAY DIFFRACTIONr_long_range_B_refined7.68257.5316858
X-RAY DIFFRACTIONr_long_range_B_other7.68557.4526831
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 301 -
Rwork0.371 5545 -
obs--98.77 %
Refinement TLS params.Method: refined / Origin x: 4.837 Å / Origin y: -17.373 Å / Origin z: -31.465 Å
111213212223313233
T0.0564 Å20.0244 Å20.0062 Å2-0.0859 Å2-0.0313 Å2--0.0441 Å2
L0.033 °2-0.0078 °2-0.0295 °2-0.1005 °20.2931 °2--0.9136 °2
S-0.0388 Å °0 Å °-0.0202 Å °0.0239 Å °0.0583 Å °-0.003 Å °0.0828 Å °0.145 Å °-0.0195 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 927
2X-RAY DIFFRACTION1A1001

+
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