[English] 日本語
Yorodumi
- PDB-8sms: Crosslinked Crystal Structure of Type II Fatty Acid Synthase, Fab... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sms
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase, FabB, and cerulenin crosslinker-crypto Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 1
  • Acyl carrier protein
KeywordsBIOSYNTHETIC PROTEIN / Ketosynthase / FabB / AcpP / acyl carrier protein / cerulenin / crosslinker / crosslink / fatty acid biosynthesis / natural product
Function / homology
Function and homology information


Kdo2-lipid A biosynthetic process / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / lipid A biosynthetic process / acyl binding / acyl carrier activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
Beta-ketoacyl synthase / 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 ...Beta-ketoacyl synthase / 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 / Acyl carrier protein (ACP) / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Chem-G7U / Acyl carrier protein / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Atlantibacter hermannii NBRC 105704 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsJiang, Z. / Chen, A. / Chen, J. / Sekhon, A. / Louie, G.V. / Noel, J.P. / La Clair, J.J. / Burkart, M.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Chem Sci / Year: 2023
Title: Masked cerulenin enables a dual-site selective protein crosslink.
Authors: Jiang, Z. / Chen, A. / Chen, J. / Sekhon, A. / Louie, G.V. / Noel, J.P. / La Clair, J.J. / Burkart, M.D.
History
DepositionApr 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 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: 3-oxoacyl-[acyl-carrier-protein] synthase 1
B: 3-oxoacyl-[acyl-carrier-protein] synthase 1
C: Acyl carrier protein
D: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3286
Polymers102,2214
Non-polymers1,1072
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-56 kcal/mol
Surface area31520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.030, 100.230, 78.310
Angle α, β, γ (deg.)90.00, 109.34, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 1 / 3-oxoacyl-[acyl-carrier-protein] synthase I / Beta-ketoacyl-ACP synthase I / KAS I


Mass: 42596.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: fabB, fabC, b2323, JW2320
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0A953, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Protein Acyl carrier protein


Mass: 8514.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Atlantibacter hermannii NBRC 105704 (bacteria)
Gene: acpP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: H5V184
#3: Chemical ChemComp-G7U / N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-{2-[(2R)-2-hydroxy-4-oxododecanamido]ethyl}-beta-alaninamide


Mass: 553.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H44N3O10P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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 Matthews: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop
Details: 26% PEG 8000, 0.3M sodium acetate, 0.1 M sodium cacodylate pH 6.0,

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→37.25 Å / Num. obs: 63659 / % possible obs: 98.6 % / Redundancy: 6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.076 / Rrim(I) all: 0.188 / Χ2: 0.98 / Net I/σ(I): 7.7 / Num. measured all: 384446
Reflection shellResolution: 1.93→1.98 Å / % possible obs: 97.1 % / Redundancy: 5.4 % / Rmerge(I) obs: 1.381 / Num. measured all: 22988 / Num. unique obs: 4228 / CC1/2: 0.65 / Rpim(I) all: 0.64 / Rrim(I) all: 1.527 / Χ2: 0.97 / Net I/σ(I) obs: 1.5

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→37.25 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2551 3057 4.8 %
Rwork0.2016 --
obs0.2042 63627 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→37.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7131 0 72 248 7451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.046
X-RAY DIFFRACTIONf_dihedral_angle_d7.1931097
X-RAY DIFFRACTIONf_chiral_restr0.061140
X-RAY DIFFRACTIONf_plane_restr0.0091331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.960.36171190.3162718X-RAY DIFFRACTION96
1.96-1.990.36351470.29882705X-RAY DIFFRACTION99
1.99-2.030.36021230.29062785X-RAY DIFFRACTION99
2.03-2.060.3311590.2782725X-RAY DIFFRACTION99
2.06-2.10.33991630.28652733X-RAY DIFFRACTION99
2.1-2.150.35911460.26662750X-RAY DIFFRACTION99
2.15-2.190.30481500.26072760X-RAY DIFFRACTION99
2.19-2.240.33291490.25442710X-RAY DIFFRACTION98
2.24-2.30.30541420.25442690X-RAY DIFFRACTION97
2.3-2.360.29921190.23582779X-RAY DIFFRACTION99
2.36-2.430.30991370.23512761X-RAY DIFFRACTION99
2.43-2.510.28571540.22472751X-RAY DIFFRACTION99
2.51-2.60.29861150.21282759X-RAY DIFFRACTION99
2.6-2.70.28971510.20962768X-RAY DIFFRACTION98
2.7-2.830.281170.21972710X-RAY DIFFRACTION97
2.83-2.980.27521580.2042771X-RAY DIFFRACTION99
2.98-3.160.23111310.18992773X-RAY DIFFRACTION99
3.16-3.410.24541350.18332764X-RAY DIFFRACTION99
3.41-3.750.24491310.17322767X-RAY DIFFRACTION98
3.75-4.290.18371220.1462820X-RAY DIFFRACTION99
4.29-5.40.15991610.13872725X-RAY DIFFRACTION98
5.4-37.250.18431280.16072846X-RAY DIFFRACTION99

+
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