[English] 日本語
Yorodumi
- PDB-3il5: Structure of E. faecalis FabH in complex with 2-({4-bromo-3-[(die... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3il5
TitleStructure of E. faecalis FabH in complex with 2-({4-bromo-3-[(diethylamino)sulfonyl]benzoyl}amino)benzoic acid
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / FabH / fatty acid biosynthesis / antibiotic / Acyltransferase / Cytoplasm / Lipid synthesis / Multifunctional enzyme
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 biosynthetic process / cytoplasm
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
Chem-B82 / Beta-ketoacyl-[acyl-carrier-protein] synthase III
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGajiwala, K.S. / Margosiak, S. / Lu, J. / Cortez, J. / Su, Y. / Nie, Z. / Appelt, K.
CitationJournal: Febs Lett. / Year: 2009
Title: Crystal structures of bacterial FabH suggest a molecular basis for the substrate specificity of the enzyme.
Authors: Gajiwala, K.S. / Margosiak, S. / Lu, J. / Cortez, J. / Su, Y. / Nie, Z. / Appelt, K.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 3-oxoacyl-[acyl-carrier-protein] synthase 3
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,4758
Polymers150,6544
Non-polymers1,8214
Water2,306128
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2384
Polymers75,3272
Non-polymers9112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint-45 kcal/mol
Surface area21920 Å2
MethodPISA
2
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2384
Polymers75,3272
Non-polymers9112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-44 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.586, 84.973, 114.390
Angle α, β, γ (deg.)90.00, 98.50, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III / KAS III


Mass: 37663.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: EF_2885, fabH / Production host: Escherichia coli (E. coli)
References: UniProt: Q820T1, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical
ChemComp-B82 / 2-({[4-bromo-3-(diethylsulfamoyl)phenyl]carbonyl}amino)benzoic acid / 2-({4-bromo-3-[(diethylamino)sulfonyl]benzoyl}amino)benzoic acid


Mass: 455.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19BrN2O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 288K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 38916 / Num. obs: 38358 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 11.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3767 / Rsym value: 0.338 / % possible all: 97.3

-
Processing

Software
NameClassification
MAR345dtbdata collection
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IL9

3il9


Resolution: 2.6→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 3691 -Random
Rwork0.1891 ---
all0.191 38916 --
obs-38358 94.4 %-
Displacement parametersBiso max: 123.34 Å2 / Biso mean: 43.762 Å2 / Biso min: 12.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.099 Å20 Å20.033 Å2
2---0.594 Å20 Å2
3---0.495 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9838 0 108 128 10074
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.2161.5
X-RAY DIFFRACTIONc_scbond_it1.8782
X-RAY DIFFRACTIONc_mcangle_it2.0392
X-RAY DIFFRACTIONc_scangle_it2.8092.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.387 580 -
Rwork0.305 --
obs-5470 86.1 %

+
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