[English] 日本語
Yorodumi
- PDB-3k8x: Crystal structure of the carboxyltransferase domain of acetyl-coe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3k8x
TitleCrystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase in complex with tepraloxydim
ComponentsAcetyl-CoA carboxylase
KeywordsTRANSFERASE / ACETYL-COA CARBOXYLASE / CARBOXYLTRANSFERASE / ACC / CT / tepraloxydim / ATP-binding / Biotin / Fatty acid biosynthesis / Ligase / Lipid synthesis / Manganese / Metal-binding / Multifunctional enzyme / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process ...Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / biotin carboxylase / acetyl-CoA carboxylase complex / biotin carboxylase activity / malonyl-CoA biosynthetic process / acetyl-CoA biosynthetic process / acetyl-CoA carboxylase activity / long-chain fatty acid biosynthetic process / fatty acid biosynthetic process / protein import into nucleus / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal ...ClpP/crotonase fold / Biotin dependent carboxylase carboxyltransferase / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / ClpP/crotonase-like domain superfamily / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-B89 / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsXiang, S. / Callaghan, M.M. / Watson, K.G. / Tong, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: A different mechanism for the inhibition of the carboxyltransferase domain of acetyl-coenzyme A carboxylase by tepraloxydim.
Authors: Xiang, S. / Callaghan, M.M. / Watson, K.G. / Tong, L.
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl-CoA carboxylase
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,6586
Polymers257,6323
Non-polymers1,0253
Water23,4741303
1
A: Acetyl-CoA carboxylase
hetero molecules

A: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,4394
Polymers171,7552
Non-polymers6842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11400 Å2
ΔGint-90 kcal/mol
Surface area58190 Å2
MethodPISA
2
B: Acetyl-CoA carboxylase
C: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,4394
Polymers171,7552
Non-polymers6842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-92 kcal/mol
Surface area56290 Å2
MethodPISA
3
C: Acetyl-CoA carboxylase
hetero molecules

A: Acetyl-CoA carboxylase
B: Acetyl-CoA carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,6586
Polymers257,6323
Non-polymers1,0253
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-17 kcal/mol
Surface area97580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)247.303, 124.797, 145.369
Angle α, β, γ (deg.)90.000, 94.320, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Acetyl-CoA carboxylase / ACC / Biotin carboxylase


Mass: 85877.461 Da / Num. of mol.: 3 / Fragment: residues 1476-2233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ACC1, ACETYL-COA CARBOXYLASE, FAS3, N3175, YNR016C / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta
References: UniProt: Q00955, acetyl-CoA carboxylase, biotin carboxylase
#2: Chemical ChemComp-B89 / (5S)-2-[(1E)-N-{[(2E)-3-chloroprop-2-en-1-yl]oxy}propanimidoyl]-3-hydroxy-5-(tetrahydro-2H-pyran-4-yl)cyclohex-2-en-1-one / tepraloxydim


Mass: 341.830 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H24ClNO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1303 / 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: 4.34 Å3/Da / Density % sol: 71.67 %
Crystal growTemperature: 276 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 8% (w/v) PEG 8000, 10% (v/v) glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 276K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2009
RadiationMonochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 192220 / Num. obs: 190725 / % possible obs: 99.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 1.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.8 / Num. unique all: 18803 / Rsym value: 0.414 / % possible all: 97.5

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.35 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 9659 5 %RANDOM
Rwork0.187 ---
obs0.189 -98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 367.84 Å2 / Biso mean: 39.72 Å2 / Biso min: 12.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20.02 Å2
2--1.97 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16321 0 69 1303 17693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02216757
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.9622694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46252039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00623.796814
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.281152867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.62715137
X-RAY DIFFRACTIONr_chiral_restr0.1180.22451
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112857
X-RAY DIFFRACTIONr_mcbond_it0.8771.510148
X-RAY DIFFRACTIONr_mcangle_it1.645216392
X-RAY DIFFRACTIONr_scbond_it2.32136609
X-RAY DIFFRACTIONr_scangle_it3.8064.56302
LS refinement shellResolution: 2.3→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 687 -
Rwork0.259 12288 -
all-12975 -
obs--91.21 %

+
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