[English] 日本語
Yorodumi
- PDB-3r1f: Crystal structure of a key regulator of virulence in Mycobacteriu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r1f
TitleCrystal structure of a key regulator of virulence in Mycobacterium tuberculosis
ComponentsESX-1 secretion-associated regulator EspR
KeywordsTRANSCRIPTION / helix-turn-helix / transcription factor / helix-turn-helix transcription factor
Function / homology
Function and homology information


response to host immune response / nucleoid / regulation of protein secretion / peptidoglycan-based cell wall / regulation of DNA-templated transcription / DNA binding / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2310 / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoid-associated protein EspR / Nucleoid-associated protein EspR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsRosenberg, O.S. / Dovey, C. / Finer-Moore, J. / Stroud, R.M. / Cox, J.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: EspR, a key regulator of Mycobacterium tuberculosis virulence, adopts a unique dimeric structure among helix-turn-helix proteins.
Authors: Rosenberg, O.S. / Dovey, C. / Tempesta, M. / Robbins, R.A. / Finer-Moore, J.S. / Stroud, R.M. / Cox, J.S.
History
DepositionMar 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references
Revision 1.2Aug 31, 2011Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ESX-1 secretion-associated regulator EspR
B: ESX-1 secretion-associated regulator EspR
C: ESX-1 secretion-associated regulator EspR
D: ESX-1 secretion-associated regulator EspR
E: ESX-1 secretion-associated regulator EspR
F: ESX-1 secretion-associated regulator EspR
G: ESX-1 secretion-associated regulator EspR
H: ESX-1 secretion-associated regulator EspR
I: ESX-1 secretion-associated regulator EspR
J: ESX-1 secretion-associated regulator EspR
K: ESX-1 secretion-associated regulator EspR
L: ESX-1 secretion-associated regulator EspR
M: ESX-1 secretion-associated regulator EspR
N: ESX-1 secretion-associated regulator EspR
O: ESX-1 secretion-associated regulator EspR
P: ESX-1 secretion-associated regulator EspR
Q: ESX-1 secretion-associated regulator EspR
R: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)273,39318
Polymers273,39318
Non-polymers00
Water34219
1
A: ESX-1 secretion-associated regulator EspR
B: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)30,3772
Polymers30,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-24 kcal/mol
Surface area13210 Å2
MethodPISA
2
C: ESX-1 secretion-associated regulator EspR
D: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)30,3772
Polymers30,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-25 kcal/mol
Surface area13080 Å2
MethodPISA
3
E: ESX-1 secretion-associated regulator EspR
F: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)30,3772
Polymers30,3772
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-25 kcal/mol
Surface area13350 Å2
MethodPISA
4
G: ESX-1 secretion-associated regulator EspR
H: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)30,3772
Polymers30,3772
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-22 kcal/mol
Surface area13230 Å2
MethodPISA
5
I: ESX-1 secretion-associated regulator EspR
J: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)30,3772
Polymers30,3772
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-22 kcal/mol
Surface area13380 Å2
MethodPISA
6
K: ESX-1 secretion-associated regulator EspR
L: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)30,3772
Polymers30,3772
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-23 kcal/mol
Surface area13230 Å2
MethodPISA
7
M: ESX-1 secretion-associated regulator EspR
N: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)30,3772
Polymers30,3772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-27 kcal/mol
Surface area13050 Å2
MethodPISA
8
O: ESX-1 secretion-associated regulator EspR
P: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)30,3772
Polymers30,3772
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-7 kcal/mol
Surface area9840 Å2
MethodPISA
9
Q: ESX-1 secretion-associated regulator EspR
R: ESX-1 secretion-associated regulator EspR


Theoretical massNumber of molelcules
Total (without water)30,3772
Polymers30,3772
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-25 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.490, 148.490, 129.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
ESX-1 secretion-associated regulator EspR


Mass: 15188.502 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: espR, MT3964, Rv3849 / Plasmid: N-terminal MBP-his-fusion / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96228, UniProt: P9WJB7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.02 Å3/Da / Density % sol: 59.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 35% 5/4 PO/OH, 50 mM Hepes, 300 mM NaCl, VAPOR DIFFUSION, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11589 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2010
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11589 Å / Relative weight: 1
ReflectionResolution: 2.5→48.85 Å / Num. all: 108207 / Num. obs: 104042

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementResolution: 2.5→48.836 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1.97 / Phase error: 25.74 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2316 5413 5.37 %
Rwork0.1969 --
obs0.1984 100721 91.05 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.348 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2748 Å2-0 Å2-0 Å2
2--3.2748 Å20 Å2
3----6.5497 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17189 0 0 19 17208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117520
X-RAY DIFFRACTIONf_angle_d1.24923678
X-RAY DIFFRACTIONf_dihedral_angle_d16.7456556
X-RAY DIFFRACTIONf_chiral_restr0.0772589
X-RAY DIFFRACTIONf_plane_restr0.0063112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54310.30562410.26654467X-RAY DIFFRACTION82
2.5431-2.58940.27942560.25774581X-RAY DIFFRACTION82
2.5894-2.63920.29562620.25914526X-RAY DIFFRACTION82
2.6392-2.6930.27892300.25064628X-RAY DIFFRACTION83
2.693-2.75160.2522640.23234577X-RAY DIFFRACTION83
2.7516-2.81560.26732230.23964697X-RAY DIFFRACTION85
2.8156-2.8860.27142750.23714571X-RAY DIFFRACTION83
2.886-2.9640.27562200.23364695X-RAY DIFFRACTION85
2.964-3.05120.29522470.22694689X-RAY DIFFRACTION85
3.0512-3.14970.24212420.22114766X-RAY DIFFRACTION86
3.1497-3.26220.2912520.21014694X-RAY DIFFRACTION85
3.2622-3.39280.23592400.19224829X-RAY DIFFRACTION86
3.3928-3.54710.24322450.1914823X-RAY DIFFRACTION88
3.5471-3.73410.21052270.17564970X-RAY DIFFRACTION89
3.7341-3.96790.20492590.17344973X-RAY DIFFRACTION90
3.9679-4.27410.1922500.16095027X-RAY DIFFRACTION91
4.2741-4.70380.1792910.15434991X-RAY DIFFRACTION90
4.7038-5.38350.19472810.16294998X-RAY DIFFRACTION91
5.3835-6.7790.24572690.19645165X-RAY DIFFRACTION93
6.779-45.52010.18982640.17785011X-RAY DIFFRACTION91

+
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