[English] 日本語
Yorodumi
- PDB-4xl4: Crystal structure of thiolase from Clostridium acetobutylicum in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xl4
TitleCrystal structure of thiolase from Clostridium acetobutylicum in complex with CoA
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


N-acetylornithine carbamoyltransferase activity / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity
Similarity search - Function
Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase ...Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Acetyl-CoA acetyltransferase / :
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Lim, J.H. / Kim, K.J.
CitationJournal: Nat Commun / Year: 2015
Title: Redox-switch regulatory mechanism of thiolase from Clostridium acetobutylicum
Authors: Kim, S. / Jang, Y.S. / Ha, S.C. / Ahn, J.W. / Kim, E.J. / Hong Lim, J. / Cho, C. / Shin Ryu, Y. / Kuk Lee, S. / Lee, S.Y. / Kim, K.J.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: PDBJ
SupersessionOct 7, 2015ID: 4N46
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Derived calculations
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,87111
Polymers84,6912
Non-polymers2,1809
Water11,458636
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-22 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.307, 54.171, 73.112
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsbiological unit is the same as asym.

-
Components

#1: Protein Acetyl-CoA acetyltransferase


Mass: 42345.496 Da / Num. of mol.: 2 / Mutation: C378S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (strain EA 2018) (bacteria)
Strain: EA 2018 / Gene: CEA_G2880 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: F0K5D8, UniProt: A0A0R4I970*PLUS, acetyl-CoA C-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: PEG 3350, K-citrate, NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 23, 2014
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 65291 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 33.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 6 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 5.6 / Rejects: 0 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N45

4n45


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.1776 / WRfactor Rwork: 0.1383 / FOM work R set: 0.9105 / SU B: 2.525 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1177 / SU Rfree: 0.1155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 3291 5.1 %RANDOM
Rwork0.142 61614 --
obs0.1441 61614 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.3 Å2 / Biso mean: 24.167 Å2 / Biso min: 10.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-0 Å2
2--0.5 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 138 636 6558
Biso mean--37.9 33.59 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196040
X-RAY DIFFRACTIONr_bond_other_d0.0010.025970
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.9928160
X-RAY DIFFRACTIONr_angle_other_deg0.899313767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3035790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48225.625224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.872151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3321524
X-RAY DIFFRACTIONr_chiral_restr0.1210.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021228
X-RAY DIFFRACTIONr_mcbond_it1.942.0433154
X-RAY DIFFRACTIONr_mcbond_other1.942.0423153
X-RAY DIFFRACTIONr_mcangle_it2.6973.0533946
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 230 -
Rwork0.172 4384 -
all-4614 -
obs--97.47 %

+
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