[English] 日本語
Yorodumi
- PDB-2nx4: The Crystal Structure of athe Putative TetR-family transcriptiona... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nx4
TitleThe Crystal Structure of athe Putative TetR-family transcriptional regulator Rha06780 from Rhodococcus sp. Rha1.
ComponentsTranscriptional regulator, TetR family protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / tetR / HTH DNA binding motif / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


BetI-type transcriptional repressor, C-terminal / BetI-type transcriptional repressor, C-terminal / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, TetR family protein
Similarity search - Component
Biological speciesRhodococcus sp. RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsZhang, R. / Evdokimova, E. / Kudritskam, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2006
Title: The Crystal Structure of a TetR-family transcriptional regulator from Rhodococcus sp.
Authors: Zhang, R. / Evdokimova, E. / Kudritskam, M. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionNov 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator, TetR family protein
B: Transcriptional regulator, TetR family protein
C: Transcriptional regulator, TetR family protein
D: Transcriptional regulator, TetR family protein


Theoretical massNumber of molelcules
Total (without water)87,0514
Polymers87,0514
Non-polymers00
Water11,007611
1
A: Transcriptional regulator, TetR family protein
B: Transcriptional regulator, TetR family protein


Theoretical massNumber of molelcules
Total (without water)43,5252
Polymers43,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-25 kcal/mol
Surface area16680 Å2
MethodPISA
2
C: Transcriptional regulator, TetR family protein
D: Transcriptional regulator, TetR family protein


Theoretical massNumber of molelcules
Total (without water)43,5252
Polymers43,5252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-26 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.439, 114.826, 73.519
Angle α, β, γ (deg.)90.00, 110.08, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein exist as dimer. There are two dimers (A/B, C/D) in the asymmetric unit.

-
Components

#1: Protein
Transcriptional regulator, TetR family protein


Mass: 21762.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. RHA1 (bacteria) / Strain: Rha1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0SCU8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.2M Ammonium Formate, 26% PEG3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.7→69.01 Å / Num. all: 88630 / Num. obs: 85617 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.46
Reflection shellResolution: 1.7→1.742 Å / Redundancy: 2 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.2 / Num. unique all: 6412 / % possible all: 79.15

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.241 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.108 / ESU R Free: 0.106
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21831 4513 5 %RANDOM
Rwork0.18526 ---
obs0.18691 85617 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.284 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20.25 Å2
2---0.75 Å20 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.042 Å0.035 Å
Luzzati d res low-6 Å
Luzzati sigma a0.6 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 0 611 6587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216050
X-RAY DIFFRACTIONr_angle_refined_deg1.1231.9598168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4255758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84523.595306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.286151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9731572
X-RAY DIFFRACTIONr_chiral_restr0.080.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024596
X-RAY DIFFRACTIONr_nbd_refined0.2040.23290
X-RAY DIFFRACTIONr_nbtor_refined0.2940.24325
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2532
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.230
X-RAY DIFFRACTIONr_mcbond_it0.7381.53913
X-RAY DIFFRACTIONr_mcangle_it1.20626024
X-RAY DIFFRACTIONr_scbond_it2.42732425
X-RAY DIFFRACTIONr_scangle_it3.8044.52144
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 286 -
Rwork0.261 5075 -
obs--79.15 %
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)
10.89150.080.35460.4461-0.04720.585-0.02060.0667-0.05830.05350.01230.01860.0432-0.0070.0083-0.03850.00060.038-0.0283-0.0102-0.027218.52549.80554.999
21.0312-0.658-0.45771.10420.27170.2038-0.1503-0.10740.13430.33660.1255-0.167-0.00140.04930.02480.09030.0453-0.0659-0.024-0.0161-0.058521.95367.61270.528
30.6288-0.467-0.16471.6905-0.15441.23960.02050.02450.0466-0.0813-0.0051-0.1580.01710.1434-0.0153-0.0240.02050.0283-0.03350.0085-0.050931.21974.35829.173
40.67150.287-0.27682.3972-0.36761.22050.00480.05490.04610.02720.09430.38170.0082-0.1619-0.0991-0.05170.02560.0241-0.02370.0292-0.01699.68570.72335.854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1002 - 101
2X-RAY DIFFRACTION1AA101 - 193102 - 194
3X-RAY DIFFRACTION2BB1 - 1002 - 101
4X-RAY DIFFRACTION2BB101 - 193102 - 194
5X-RAY DIFFRACTION3CC7 - 1008 - 101
6X-RAY DIFFRACTION3CC101 - 193102 - 194
7X-RAY DIFFRACTION4DD7 - 1008 - 101
8X-RAY DIFFRACTION4DD101 - 193102 - 194

+
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://pdbjlvh1.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