[English] 日本語
Yorodumi
- PDB-1hnk: CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III, APO TETRAGON... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hnk
TitleCRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III, APO TETRAGONAL FORM
ComponentsBETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III
KeywordsTRANSFERASE / fabh
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid metabolic process / fatty acid biosynthetic process / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsQiu, X. / Janson, C.A. / Smith, W.W. / Head, M. / Lonsdale, J. / Konstantinidis, A.K.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Refined structures of beta-ketoacyl-acyl carrier protein synthase III.
Authors: Qiu, X. / Janson, C.A. / Smith, W.W. / Head, M. / Lonsdale, J. / Konstantinidis, A.K.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Crystal Structure of Beta-Ketoacyl-Acyl Carrier Protein Synthase III. A Key Condensing Enzyme in Bacterial Fatty Acid Biosynthesis
Authors: Qiu, X. / Janson, C.A. / Konstantinidis, A.K. / Nwagwu, S. / Silverman, C. / Smith, W.W. / Khandekar, S.K. / Lonsdale, J. / Abdel-Meguid, S.S.
History
DepositionDec 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: 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: BETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III


Theoretical massNumber of molelcules
Total (without water)33,5471
Polymers33,5471
Non-polymers00
Water1,802100
1
A: BETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III

A: BETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III


Theoretical massNumber of molelcules
Total (without water)67,0942
Polymers67,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2400 Å2
ΔGint-14 kcal/mol
Surface area20360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.650, 72.650, 99.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-499-

HOH

-
Components

#1: Protein BETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE III / 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III / BETA-KETOACYL-ACP SYNTHASE III


Mass: 33547.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6R0, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion / Details: Janson, C.A., (2000) Acta Crystallogr.D, 56, 747.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
350 mM1dropNaCl
42 mMdithiothreitol1drop
50.1 Mmagnesium chloride1reservoir
60.05 MTris-HCl1reservoir
715 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 303763 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 %
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / Num. unique all: 17875 / % possible all: 100
Reflection
*PLUS
Num. obs: 40226 / Num. measured all: 303763 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 100 %

-
Processing

Software
NameClassification
CNSrefinement
CORELSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1HN9

1hn9


Resolution: 1.9→20 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.24 2000 5%
Rwork0.204 --
obs-40226 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 100 2070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
Software
*PLUS
Name: CORELS / Classification: refinement
Refinement
*PLUS
Num. reflection all: 40226 / Num. reflection obs: 17875
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_angle_deg

+
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