[English] 日本語
Yorodumi
- PDB-4f6c: Crystal structure of Aureusimine biosynthetic cluster reductase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f6c
TitleCrystal structure of Aureusimine biosynthetic cluster reductase domain
ComponentsAusA reductase domain protein
KeywordsOXIDOREDUCTASE / Thioester reductase
Function / homology
Function and homology information


: / acyltransferase activity / catalytic activity / antibiotic biosynthetic process / fatty acid metabolic process / oxidoreductase activity
Similarity search - Function
Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site ...Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative long chain fatty acid-CoA ligase VraA / Putative long chain fatty acid-CoA ligase VraA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.812 Å
AuthorsMok, M. / Junop, M.
CitationJournal: Chembiochem / Year: 2012
Title: Heterologous expression and structural characterisation of a pyrazinone natural product assembly line.
Authors: Wyatt, M.A. / Mok, M.C. / Junop, M. / Magarvey, N.A.
History
DepositionMay 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AusA reductase domain protein
B: AusA reductase domain protein


Theoretical massNumber of molelcules
Total (without water)99,1002
Polymers99,1002
Non-polymers00
Water724
1
A: AusA reductase domain protein


Theoretical massNumber of molelcules
Total (without water)49,5501
Polymers49,5501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AusA reductase domain protein


Theoretical massNumber of molelcules
Total (without water)49,5501
Polymers49,5501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.699, 106.446, 124.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein AusA reductase domain protein


Mass: 49550.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: SAV0179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99X42, UniProt: A0A0H3JX00*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M tri-sodium citrate, 0.1 M HEPES pH 7.5, 10% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2010
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 27.1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.812→44.427 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 26.28 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2427 1935 5.78 %random
Rwork0.2057 ---
all0.2078 33500 --
obs0.2078 33500 95.86 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.381 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-26.0772 Å2-0 Å2-0 Å2
2---16.0196 Å2-0 Å2
3----13.7084 Å2
Refinement stepCycle: LAST / Resolution: 2.812→44.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5541 0 0 4 5545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095643
X-RAY DIFFRACTIONf_angle_d1.1777696
X-RAY DIFFRACTIONf_dihedral_angle_d15.5171944
X-RAY DIFFRACTIONf_chiral_restr0.08927
X-RAY DIFFRACTIONf_plane_restr0.004975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.812-2.88220.43091190.3411985X-RAY DIFFRACTION85
2.8822-2.96010.31691350.29082137X-RAY DIFFRACTION93
2.9601-3.04720.29751400.26842149X-RAY DIFFRACTION93
3.0472-3.14560.29831390.24652180X-RAY DIFFRACTION95
3.1456-3.25790.25871350.23622199X-RAY DIFFRACTION95
3.2579-3.38830.31691380.232216X-RAY DIFFRACTION95
3.3883-3.54250.22891330.20532234X-RAY DIFFRACTION96
3.5425-3.72920.25181360.19332275X-RAY DIFFRACTION97
3.7292-3.96270.23561410.18512292X-RAY DIFFRACTION98
3.9627-4.26840.19961400.16572310X-RAY DIFFRACTION99
4.2684-4.69750.20751360.15872353X-RAY DIFFRACTION99
4.6975-5.37630.22481420.18432369X-RAY DIFFRACTION100
5.3763-6.76970.25381470.23122394X-RAY DIFFRACTION100
6.7697-44.43220.23091540.21342472X-RAY DIFFRACTION98

+
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