[English] 日本語
Yorodumi
- PDB-1w96: Crystal Structure of Biotin Carboxylase Domain of Acetyl-coenzyme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w96
TitleCrystal Structure of Biotin Carboxylase Domain of Acetyl-coenzyme A Carboxylase from Saccharomyces cerevisiae in Complex with Soraphen A
ComponentsACETYL-COENZYME A CARBOXYLASE
KeywordsLIGASE / OBESITY / DIABETES / FATTY ACID METABOLISM / STRUCTURE-BASED DRUG DESIGN / ALLOSTERIC INHIBITION / POLYKETIDE
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 / acetyl-CoA carboxylase complex / biotin carboxylase / malonyl-CoA biosynthetic process / acetyl-CoA biosynthetic process ...Biotin transport and metabolism / Fatty acyl-CoA biosynthesis / Carnitine shuttle / acetyl-CoA carboxylase / carboxyl- or carbamoyltransferase activity / acetyl-CoA binding / acetyl-CoA carboxylase complex / biotin carboxylase / malonyl-CoA biosynthetic process / acetyl-CoA biosynthetic process / biotin carboxylase activity / acetyl-CoA carboxylase activity / long-chain fatty acid biosynthetic process / protein import into nucleus / fatty acid biosynthetic process / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
PreATP-grasp fold / PreATP-grasp domain / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase ...PreATP-grasp fold / PreATP-grasp domain / Acetyl-CoA carboxylase, central domain / : / : / Acetyl-CoA carboxylase, central region / Acetyl-CoA carboxylase, BT domain / Acetyl-coenzyme A carboxyltransferase, N-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile. / Acetyl-CoA carboxylase / Carboxyl transferase domain / Rossmann fold - #20 / Acetyl-coenzyme A carboxyltransferase, C-terminal / Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile. / 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 / ATP-grasp fold, A 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 / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Dna Ligase; domain 1 / Carbamoyl-phosphate synthase subdomain signature 2. / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SORAPHEN A / Acetyl-CoA carboxylase
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsShen, Y. / Volrath, S.L. / Weatherly, S.C. / Elich, T.D. / Tong, L.
CitationJournal: Mol.Cell / Year: 2004
Title: A Mechanism for the Potent Inhibition of Eukaryotic Acetyl-Coenzyme a Carboxylase by Soraphen A, a Macrocyclic Polyketide Natural Product
Authors: Shen, Y. / Volrath, S.L. / Weatherly, S.C. / Elich, T.D. / Tong, L.
History
DepositionOct 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACETYL-COENZYME A CARBOXYLASE
B: ACETYL-COENZYME A CARBOXYLASE
C: ACETYL-COENZYME A CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,5196
Polymers184,9573
Non-polymers1,5623
Water26,0321445
1
A: ACETYL-COENZYME A CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1732
Polymers61,6521
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ACETYL-COENZYME A CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1732
Polymers61,6521
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: ACETYL-COENZYME A CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1732
Polymers61,6521
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.830, 96.520, 139.950
Angle α, β, γ (deg.)90.00, 96.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.34576, 0.81813, 0.45947), (-0.8201, -0.50143, 0.2757), (0.45595, -0.28148, 0.84432)-9.90431, 80.52773, 33.51553
3given(0.32725, -0.82537, -0.46009), (-0.82615, -0.48625, 0.28467), (-0.45867, 0.28694, -0.841)119.09418, 80.04326, 217.49756

-
Components

#1: Protein ACETYL-COENZYME A CARBOXYLASE / ACC


Mass: 61652.352 Da / Num. of mol.: 3 / Fragment: BIOTIN CARBOXYLASE DOMAIN, RESIDUES 13-566
Source method: isolated from a genetically manipulated source
Details: POLYKETIDE SORAPHEN A
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q00955, acetyl-CoA carboxylase
#2: Chemical ChemComp-S1A / SORAPHEN A


Mass: 520.655 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H44O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1445 / 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: 2.22 Å3/Da / Density % sol: 44.1 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.978994,0.979232, 0.970227
DetectorDate: Mar 30, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9789941
20.9792321
30.9702271
ReflectionResolution: 1.8→29.2 Å / Num. obs: 150099 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 88

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKLdata reduction
HKLdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.2 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 371358.73 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 11219 7.5 %RANDOM
Rwork0.195 ---
obs0.195 150099 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.7639 Å2 / ksol: 0.376114 e/Å3
Displacement parametersBiso mean: 26.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20 Å2-0.3 Å2
2---1.31 Å20 Å2
3----2.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12726 0 111 1445 14282
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.283 1018 7.5 %
Rwork0.258 12641 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5SOR.PARSOR.TOP

+
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