[English] 日本語
Yorodumi
- PDB-1b3n: BETA-KETOACYL CARRIER PROTEIN SYNTHASE AS A DRUG TARGET, IMPLICAT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b3n
TitleBETA-KETOACYL CARRIER PROTEIN SYNTHASE AS A DRUG TARGET, IMPLICATIONS FROM THE CRYSTAL STRUCTURE OF A COMPLEX WITH THE INHIBITOR CERULENIN.
ComponentsPROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)
KeywordsCONDENSING ENZYMES / FATTY ACID ELONGATION / CERULENIN INHIBITION / LIPID METABOLISM / DRUG DESIGN / DRUG TARGET
Function / homology
Function and homology information


fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / response to cold / fatty acid biosynthetic process / protein homodimerization activity / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CER / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.65 Å
AuthorsMoche, M. / Schneider, G. / Edwards, P. / Dehesh, K. / Lindqvist, Y.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Structure of the complex between the antibiotic cerulenin and its target, beta-ketoacyl-acyl carrier protein synthase.
Authors: Moche, M. / Schneider, G. / Edwards, P. / Dehesh, K. / Lindqvist, Y.
History
DepositionDec 14, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1842
Polymers42,9581
Non-polymers2251
Water95553
1
A: PROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)
hetero molecules

A: PROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3674
Polymers85,9172
Non-polymers4512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7360 Å2
ΔGint-47 kcal/mol
Surface area26310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.394, 76.394, 147.675
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein PROTEIN (KETOACYL ACYL CARRIER PROTEIN SYNTHASE 2)


Mass: 42958.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: FABF / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[PREP4]
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-CER / (2S, 3R)-3-HYDROXY-4-OXO-7,10-TRANS,TRANS-DODECADIENAMIDE / CERULENIN


Mass: 225.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO3 / Comment: antifungal, antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE CERULENIN RESIDUE IS GIVEN CHAIN IDENTIFIER A AND RESIDUE NUMBER 413.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growpH: 8
Details: 5.6 MG/ML KAS-CERULENIN COMPLEX IN 0.3M NACL, 25MM TRIS PH8.0, 5MM IMIDAZOLE AND 10% (V/V) GLYCEROL WERE MIXED (2+2UL) WITH A 1000 UL RESERVOIR SOLUTION CONSISTING OF 26% W/V PEG8000 0.1% ...Details: 5.6 MG/ML KAS-CERULENIN COMPLEX IN 0.3M NACL, 25MM TRIS PH8.0, 5MM IMIDAZOLE AND 10% (V/V) GLYCEROL WERE MIXED (2+2UL) WITH A 1000 UL RESERVOIR SOLUTION CONSISTING OF 26% W/V PEG8000 0.1% V/V 2-MERCAPTOETHANOL AND WATER. CRYSTALS APPEARED IN A FEW DAYS
Components of the solutions
IDNameCrystal-IDSol-ID
15.6 MG/ML KAS-CERULENIN COMPLEX IN 0.3M NACL, 25MM TRIS PH8.0, 5MM IMIDAZOLE AND 10% (V/V) GLYCEROL11
2A 1000 UL RESERVOIR SOLUTION CONSISTING OF 26% W/V PEG8000, 0.1% V/V 2-MERCAPTOETHANOL AND WATER.12
Crystal grow
*PLUS
Temperature: 298 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
20.3 M1dropNaCl
325 mMTris-HCl1drop
45 mMimidazole1drop
510 %(v/v)glycerol1drop
626 %(w/v)PEG80001reservoir
70.1 %(v/v)2-mercaptoethanol1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.958
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.958 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 12600 / % possible obs: 83.4 % / Redundancy: 1.8 % / Rsym value: 0.095 / Net I/σ(I): 5.3
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.325 / % possible all: 71.8
Reflection
*PLUS
Num. measured all: 22896 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 71.8 % / Rmerge(I) obs: 0.325

-
Processing

Software
NameVersionClassification
SIGMAAmodel building
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
SIGMAAphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.65→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: RAMACHANDRAN PLOT, PERCENT OF NON- GLYCINE OR NON-PROLINE RESIDUES IN MOST FAVOURED REGION 88.9% ADDITIONAL ALLOWED REGION 10.5% GENEROUSLY ALLOWED REGION 0.3% DISALLOWED REGION 0.3% BOND ...Details: RAMACHANDRAN PLOT, PERCENT OF NON- GLYCINE OR NON-PROLINE RESIDUES IN MOST FAVOURED REGION 88.9% ADDITIONAL ALLOWED REGION 10.5% GENEROUSLY ALLOWED REGION 0.3% DISALLOWED REGION 0.3% BOND LENGTHS (A) : 0.008 BOND ANGLES ( DEGREES) : 1.7 DIHEDRAL ANGLES (DEGREES) : 26.2 IMPROPER ANGLES (DEGREES) : 1.8
RfactorNum. reflection% reflectionSelection details
Rfree0.27 631 5 %EVERY 20TH REFLECTION
Rwork0.213 ---
obs-22896 83.4 %-
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 16 53 3074
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11926 / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.08
X-RAY DIFFRACTIONp_angle_deg1.7
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg26.2
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_improper_angle_deg1.8

+
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