[English] 日本語
Yorodumi
- PDB-4yak: Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yak
TitleCa. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in complex with coenzyme A, acetyl-coenzyme A and with phosphorylated phosphohistidine segment (site I orientation)
Components
  • alpha subunit of Acyl-CoA synthetase (NDP forming)
  • beta subunit of Acyl-CoA synthetase (NDP forming)
KeywordsLIGASE / Dinucleotide forming acetyl-CoA synthetase / complex / ACD
Function / homology
Function and homology information


acetate-CoA ligase (ADP-forming) activity / ligase activity / nucleotide binding / ATP binding / metal ion binding
Similarity search - Function
Ligase-CoA domain / Ligase-CoA domain / : / Succinyl-CoA synthetase-like, flavodoxin domain / ATP-grasp domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase domains / Succinyl-CoA synthetase-like / CoA binding domain ...Ligase-CoA domain / Ligase-CoA domain / : / Succinyl-CoA synthetase-like, flavodoxin domain / ATP-grasp domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase domains / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / COENZYME A / Acyl-CoA synthetase (NDP forming) / ATP-grasp domain-containing protein
Similarity search - Component
Biological speciesKorarchaeum cryptofilum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.464 Å
AuthorsWeisse, R.H.-J. / Scheidig, A.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer.
Authors: Weie, R.H. / Faust, A. / Schmidt, M. / Schonheit, P. / Scheidig, A.J.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alpha subunit of Acyl-CoA synthetase (NDP forming)
B: beta subunit of Acyl-CoA synthetase (NDP forming)
C: alpha subunit of Acyl-CoA synthetase (NDP forming)
D: beta subunit of Acyl-CoA synthetase (NDP forming)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,7986
Polymers150,2214
Non-polymers1,5772
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-63 kcal/mol
Surface area52350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.410, 111.690, 125.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein alpha subunit of Acyl-CoA synthetase (NDP forming)


Mass: 49433.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: phosphohistidine His254
Source: (gene. exp.) Korarchaeum cryptofilum (strain OPF8) (archaea)
Strain: OPF8 / Gene: Kcr_0198 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L3C9
#2: Protein beta subunit of Acyl-CoA synthetase (NDP forming)


Mass: 25676.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Korarchaeum cryptofilum (strain OPF8) (archaea)
Strain: OPF8 / Gene: Kcr_0115 / Plasmid: pET17b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1L7P8
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.63 % / Description: rod-like appearance
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl pH 8.7, 14% (w/v) PEG6000, 10 mM Na2HPO4, 5 mM NaOAc

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.110.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)20.976
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELApr 18, 2013
DECTRIS PILATUS 6M2PIXELMay 17, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.9761
ReflectionResolution: 2.46→83.571 Å / Num. all: 54078 / Num. obs: 54078 / % possible obs: 98.1 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.222 / Net I/σ(I): 9.7
Reflection shellResolution: 2.46→2.53 Å / Redundancy: 6.8 % / Rmerge(I) obs: 3.423 / Mean I/σ(I) obs: 0.6 / % possible all: 77.3

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSJuly 4, 2012data reduction
XSCALENovember 3, 2014data scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CSU and 1WR2

2csu

1wr2


Resolution: 2.464→83.571 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 2721 5.07 %RANDOM
Rwork0.1936 ---
obs0.1958 53659 97.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.464→83.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10442 0 99 18 10559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610735
X-RAY DIFFRACTIONf_angle_d0.8814575
X-RAY DIFFRACTIONf_dihedral_angle_d12.7044005
X-RAY DIFFRACTIONf_chiral_restr0.0361675
X-RAY DIFFRACTIONf_plane_restr0.0041920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4635-2.50830.4204860.41391484X-RAY DIFFRACTION55
2.5083-2.55650.40311430.38632708X-RAY DIFFRACTION100
2.5565-2.60870.39811520.35282691X-RAY DIFFRACTION100
2.6087-2.66550.38651340.34792737X-RAY DIFFRACTION100
2.6655-2.72750.34531440.33752721X-RAY DIFFRACTION100
2.7275-2.79570.30821560.30592701X-RAY DIFFRACTION100
2.7957-2.87130.33061490.25862699X-RAY DIFFRACTION100
2.8713-2.95580.30651500.26322726X-RAY DIFFRACTION100
2.9558-3.05120.31391350.25512734X-RAY DIFFRACTION100
3.0512-3.16020.28911440.26352714X-RAY DIFFRACTION100
3.1602-3.28680.25481500.22412729X-RAY DIFFRACTION100
3.2868-3.43640.26091500.20472750X-RAY DIFFRACTION100
3.4364-3.61750.26891460.18542715X-RAY DIFFRACTION100
3.6175-3.84420.20211440.17252750X-RAY DIFFRACTION100
3.8442-4.1410.20471460.16642758X-RAY DIFFRACTION100
4.141-4.55770.20821490.14092758X-RAY DIFFRACTION100
4.5577-5.21710.16011450.14052787X-RAY DIFFRACTION100
5.2171-6.57260.21621450.16722827X-RAY DIFFRACTION100
6.5726-83.61950.17851530.13032949X-RAY DIFFRACTION100

+
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