[English] 日本語
Yorodumi
- PDB-5suv: Crystal structure of holo-[acyl-carrier-protein] synthase (AcpS) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5suv
TitleCrystal structure of holo-[acyl-carrier-protein] synthase (AcpS) from Neisseria meningitidis in complex with Coenzyme A
ComponentsHolo-[acyl-carrier-protein] synthase
KeywordsTRANSFERASE / acpS / FASII / trimer / CoA
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesNeisseria meningitidis FAM18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsNanson, J.D. / Forwood, J.K.
CitationJournal: To Be Published
Title: Crystal structure of holo-[acyl-carrier-protein] synthase (AcpS) from Neisseria meningitidis in complex with Coenzyme A
Authors: Nanson, J.D. / Forwood, J.K.
History
DepositionAug 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Holo-[acyl-carrier-protein] synthase
B: Holo-[acyl-carrier-protein] synthase
C: Holo-[acyl-carrier-protein] synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6006
Polymers41,2983
Non-polymers2,3033
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-35 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.507, 92.686, 92.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Holo-[acyl-carrier-protein] synthase / Holo-ACP synthase / 4'-phosphopantetheinyl transferase AcpS


Mass: 13765.921 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis FAM18 (bacteria)
Strain: ATCC 700532 / DSM 15464 / FAM18 / Gene: acpS, NMC1700 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli)
References: UniProt: A1KVH5, holo-[acyl-carrier-protein] synthase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / Details: 200 mM sodium citrate tribasic, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.951 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.951 Å / Relative weight: 1
ReflectionResolution: 1.75→46.343 Å / Num. obs: 41271 / % possible obs: 98.2 % / Redundancy: 3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.895 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX1.10pre_2104refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.343 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.56
RfactorNum. reflection% reflection
Rfree0.2279 2026 4.91 %
Rwork0.1884 --
obs0.1902 41233 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→46.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 144 264 3316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083139
X-RAY DIFFRACTIONf_angle_d0.9634247
X-RAY DIFFRACTIONf_dihedral_angle_d12.1761821
X-RAY DIFFRACTIONf_chiral_restr0.053455
X-RAY DIFFRACTIONf_plane_restr0.006528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.28021640.25382770X-RAY DIFFRACTION99
1.7938-1.84230.26361580.23812764X-RAY DIFFRACTION99
1.8423-1.89650.27491800.23252778X-RAY DIFFRACTION99
1.8965-1.95770.22541450.232776X-RAY DIFFRACTION99
1.9577-2.02770.27471190.21662799X-RAY DIFFRACTION99
2.0277-2.10890.25641570.20942801X-RAY DIFFRACTION99
2.1089-2.20480.2521300.19982812X-RAY DIFFRACTION99
2.2048-2.32110.22811440.19912806X-RAY DIFFRACTION98
2.3211-2.46650.22931380.19682797X-RAY DIFFRACTION98
2.4665-2.65690.24921490.20032804X-RAY DIFFRACTION97
2.6569-2.92420.25881220.1992792X-RAY DIFFRACTION97
2.9242-3.34730.22211320.17982816X-RAY DIFFRACTION97
3.3473-4.21680.21490.16532790X-RAY DIFFRACTION96
4.2168-46.35920.1971390.16392902X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 16.5811 Å / Origin y: 92.9984 Å / Origin z: 3.2134 Å
111213212223313233
T0.239 Å20.1109 Å20.027 Å2-0.2154 Å20.0324 Å2--0.2269 Å2
L1.0866 °2-0.2206 °2-0.3314 °2-0.9332 °2-0.5757 °2--3.3148 °2
S0.0011 Å °-0.0681 Å °-0.2328 Å °-0.1301 Å °-0.1904 Å °-0.0793 Å °0.6827 Å °0.5622 Å °0.0632 Å °
Refinement TLS groupSelection details: all

+
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