[English] 日本語
Yorodumi
- PDB-4g8x: G1 ORF67 / Staphyloccus aureus sigmaA domain 4 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4g8x
TitleG1 ORF67 / Staphyloccus aureus sigmaA domain 4 complex
Components
  • ORF067
  • RNA polymerase sigma factor rpoD
KeywordsDNA BINDING PROTEIN / RNAP binding protein
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm
Similarity search - Function
Helix Hairpins - #1800 / : / : / Phage G1 gp67, N-terminal domain / Phage G1 gp67, C-terminal domain / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal ...Helix Hairpins - #1800 / : / : / Phage G1 gp67, N-terminal domain / Phage G1 gp67, C-terminal domain / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Helix Hairpins / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase sigma factor SigA / ORF067
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
Staphylococcus phage G1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.001 Å
AuthorsDarst, S.A. / Osmundson, J.S. / Montero-Diaz, C.M. / Hochschild, A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Promoter-specific transcription inhibition in Staphylococcus aureus by a phage protein.
Authors: Osmundson, J. / Montero-Diez, C. / Westblade, L.F. / Hochschild, A. / Darst, S.A.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA polymerase sigma factor rpoD
B: ORF067
C: RNA polymerase sigma factor rpoD
D: ORF067


Theoretical massNumber of molelcules
Total (without water)61,6474
Polymers61,6474
Non-polymers00
Water0
1
A: RNA polymerase sigma factor rpoD
B: ORF067


Theoretical massNumber of molelcules
Total (without water)30,8232
Polymers30,8232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: RNA polymerase sigma factor rpoD
D: ORF067


Theoretical massNumber of molelcules
Total (without water)30,8232
Polymers30,8232
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.137, 56.951, 57.030
Angle α, β, γ (deg.)90.00, 104.79, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein RNA polymerase sigma factor rpoD


Mass: 7409.352 Da / Num. of mol.: 2 / Fragment: UNP Residues 296-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: NCTC 8325 / Gene: plaC, rpoD, SAOUHSC_01662, sigA, Sigma A domain 4 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0J0
#2: Protein ORF067


Mass: 23413.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage G1 (virus) / Gene: ORF67 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4Z9Y5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16M Calcium acetate, 0.08 M Sodium Cacodylate pH 6.5, 15% PEG 8000, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1701
2701
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.0389
SYNCHROTRONNSLS X3A20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 14, 2008
MAR CCD 165 mm2CCDJan 8, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03891
20.9791
ReflectionResolution: 3→40 Å / Num. obs: 13818 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.001→37.71 Å / SU ML: 0.5 / σ(F): 1.35 / Phase error: 36.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3277 1380 9.99 %
Rwork0.2806 --
obs0.2853 13812 99.8 %
all-13818 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.001→37.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 0 3325
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033369
X-RAY DIFFRACTIONf_angle_d0.694554
X-RAY DIFFRACTIONf_dihedral_angle_d12.2691121
X-RAY DIFFRACTIONf_chiral_restr0.051513
X-RAY DIFFRACTIONf_plane_restr0.002614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.001-3.10820.41521330.34861203X-RAY DIFFRACTION99
3.1082-3.23260.32881420.32691229X-RAY DIFFRACTION100
3.2326-3.37960.41971380.31661231X-RAY DIFFRACTION100
3.3796-3.55770.41261450.30681250X-RAY DIFFRACTION100
3.5577-3.78040.33431250.29581231X-RAY DIFFRACTION100
3.7804-4.0720.29261350.25771250X-RAY DIFFRACTION100
4.072-4.48120.28291440.25961241X-RAY DIFFRACTION100
4.4812-5.12820.36371350.26761250X-RAY DIFFRACTION100
5.1282-6.45580.32711390.31421250X-RAY DIFFRACTION100
6.4558-37.71340.30081440.25931297X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.59053.80552.53746.40753.65163.43990.54530.5086-0.8677-0.5754-0.3747-0.29790.6924-0.16650.0121.18330.1242-0.18380.732-0.22821.194535.541320.3815-6.2264
23.7704-2.4223-0.85011.77520.24964.09380.2484-0.3204-0.10710.096-0.0839-0.56240.250.0959-0.19020.8202-0.1078-0.12280.31130.10330.831853.046114.50116.3607
31.2868-0.8623-1.45222.426-1.145.7774-0.6556-0.96290.8411.18910.6605-0.33010.9204-1.9214-0.20722.0671.0976-0.02512.7494-0.9387-0.019414.822739.13226.7481
46.63411.7337-0.44085.6185-0.33634.0662-1.1869-0.54892.04082.01311.35150.9783-0.7619-1.93090.61011.26671.1219-0.3152.5836-0.3871.26063.519949.304313.0204
53.8973-0.73862.45732.3986-1.79494.376-1.3902-1.82791.34950.70820.96430.5966-1.0259-1.64670.00451.02880.3722-0.00091.6989-0.33250.867321.889137.130514.2429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain 'A'
2X-RAY DIFFRACTION2chain 'B' and ((resseq 1:92))
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D' and ((resseq 1:92))
5X-RAY DIFFRACTION5chain 'D' and ((resseq 93:198))

+
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