[English] 日本語
Yorodumi
- PDB-8g4u: Final ketosynthase+acyltransferase of the erythromycin modular po... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g4u
TitleFinal ketosynthase+acyltransferase of the erythromycin modular polyketide synthase
ComponentsEryAIII
KeywordsBIOSYNTHETIC PROTEIN / ketosynthase / acyltransferase / cerulenin / multimerization
Function / homology
Function and homology information


macrolide biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Polyketide synthase, ketoreductase domain / KR domain ...Polyketide synthase, docking domain superfmaily / Polyketide synthase, thioesterase domain / Thioesterase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Thioesterase / Thioesterase domain / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site / Thiolase-like / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKeatinge-Clay, A.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)106112 United States
CitationJournal: Biorxiv / Year: 2023
Title: Crystal structures reveal the framework of cis -acyltransferase modular polyketide synthases.
Authors: Keatinge-Clay, A.T. / Miyazawa, T. / Zhang, J. / Ray, K.A. / Lutgens, J.D. / Bista, R. / Lin, S.N.
History
DepositionFeb 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EryAIII
B: EryAIII
C: EryAIII
D: EryAIII


Theoretical massNumber of molelcules
Total (without water)363,8174
Polymers363,8174
Non-polymers00
Water1448
1
A: EryAIII
B: EryAIII


Theoretical massNumber of molelcules
Total (without water)181,9092
Polymers181,9092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: EryAIII
D: EryAIII


Theoretical massNumber of molelcules
Total (without water)181,9092
Polymers181,9092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.210, 167.940, 184.230
Angle α, β, γ (deg.)90.000, 99.430, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
EryAIII


Mass: 90954.344 Da / Num. of mol.: 4 / Mutation: A2357Q
Source method: isolated from a genetically manipulated source
Details: Ery(KS6+AT7), the final ketosynthase and acyltransferase of the erythromycin modular polyketide synthase
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: eryAIII / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5UNP4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.99 Å3/Da / Density % sol: 59 % / Description: clusters of triangular plates
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8 mg/mL Ery(KS6+AT7) was supplied with 1 mM cerulenin and added 3:1 to the well condition (10% PEG3350, 150 mM MgSO4, 150 mM NaCl, 100 mM Tris pH 7.5)

-
Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2006
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.9→76.23 Å / Num. obs: 93921 / % possible obs: 99.24 % / Redundancy: 2 % / Biso Wilson estimate: 55.22 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.1487 / Rpim(I) all: 0.1487 / Rrim(I) all: 0.2102 / Net I/σ(I): 5.36
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 2 % / Rmerge(I) obs: 1.086 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 9416 / CC1/2: 0.404 / CC star: 0.759 / Rpim(I) all: 0.1487 / % possible all: 99.61

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→76.23 Å / SU ML: 0.5196 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.4232
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3143 1725 1.84 %
Rwork0.2391 92082 -
obs0.2404 93807 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.54 Å2
Refinement stepCycle: LAST / Resolution: 2.9→76.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22979 0 0 8 22987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009623414
X-RAY DIFFRACTIONf_angle_d1.211731897
X-RAY DIFFRACTIONf_chiral_restr0.06053678
X-RAY DIFFRACTIONf_plane_restr0.01074245
X-RAY DIFFRACTIONf_dihedral_angle_d7.15753396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.42981400.35747700X-RAY DIFFRACTION99.61
2.99-3.080.40981450.34757662X-RAY DIFFRACTION99.8
3.08-3.190.43071430.31977689X-RAY DIFFRACTION99.89
3.19-3.320.41451460.2967685X-RAY DIFFRACTION99.81
3.32-3.470.34711420.26997659X-RAY DIFFRACTION99.68
3.47-3.650.33671510.24737712X-RAY DIFFRACTION99.49
3.65-3.880.28991400.23897654X-RAY DIFFRACTION99.31
3.88-4.180.29941500.22177689X-RAY DIFFRACTION98.93
4.18-4.60.26381410.19387546X-RAY DIFFRACTION98.21
4.6-5.270.28581410.20157618X-RAY DIFFRACTION98.38
5.27-6.640.29011450.22777717X-RAY DIFFRACTION99.39
6.64-76.230.24321410.19447751X-RAY DIFFRACTION98.43

+
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