[English] 日本語
Yorodumi
- PDB-3lsg: The crystal structure of the C-terminal domain of the two-compone... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lsg
TitleThe crystal structure of the C-terminal domain of the two-component response regulator yesN from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
ComponentsTwo-component response regulator yesN
KeywordsTranscription regulator / structural genomics / PSI-2 / protein structure initiative / MCSG / Midwest Center for Structural Genomics / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


phosphorelay signal transduction system / sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
Transcription regulator HTH, AraC- type / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily ...Transcription regulator HTH, AraC- type / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Two-component response regulator yesN
Similarity search - Component
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.049 Å
AuthorsTan, K. / Rakowski, E. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the C-terminal domain of the two-component response regulator yesN from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Authors: Tan, K. / Rakowski, E. / Clancy, S. / Joachimiak, A.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Two-component response regulator yesN
B: Two-component response regulator yesN
C: Two-component response regulator yesN
D: Two-component response regulator yesN
E: Two-component response regulator yesN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8396
Polymers61,7445
Non-polymers951
Water4,738263
1
A: Two-component response regulator yesN
B: Two-component response regulator yesN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7933
Polymers24,6982
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-10 kcal/mol
Surface area11350 Å2
MethodPISA
2
C: Two-component response regulator yesN
D: Two-component response regulator yesN


Theoretical massNumber of molelcules
Total (without water)24,6982
Polymers24,6982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-4 kcal/mol
Surface area11180 Å2
MethodPISA
3
E: Two-component response regulator yesN


Theoretical massNumber of molelcules
Total (without water)12,3491
Polymers12,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.224, 66.224, 245.401
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
Two-component response regulator yesN


Mass: 12348.824 Da / Num. of mol.: 5 / Fragment: C-terminal domain residues 154-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Strain: ATCC 25586 / Gene: FN0189 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q8RGT8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M di-sodium hydrogen phosphate, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 287K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97901 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2009 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2.05→37.3 Å / Num. all: 39683 / Num. obs: 39683 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 28.44 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 26.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1874 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.049→37.29 Å / SU ML: 0.24 / σ(F): 0.04 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1915 5.03 %random
Rwork0.1846 ---
obs0.1875 38080 94.25 %-
all-38080 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.543 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9916 Å20 Å20 Å2
2---0.9916 Å2-0 Å2
3---1.9833 Å2
Refinement stepCycle: LAST / Resolution: 2.049→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4197 0 5 263 4465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074278
X-RAY DIFFRACTIONf_angle_d0.9445745
X-RAY DIFFRACTIONf_dihedral_angle_d17.4631599
X-RAY DIFFRACTIONf_chiral_restr0.068634
X-RAY DIFFRACTIONf_plane_restr0.004716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0488-2.1220.29051640.2283204X-RAY DIFFRACTION85
2.122-2.2070.26091760.20853412X-RAY DIFFRACTION90
2.207-2.30740.27121790.19113429X-RAY DIFFRACTION92
2.3074-2.4290.24391830.18983570X-RAY DIFFRACTION94
2.429-2.58120.26882050.1953567X-RAY DIFFRACTION95
2.5812-2.78040.24461810.20233666X-RAY DIFFRACTION96
2.7804-3.06010.27442060.21243691X-RAY DIFFRACTION97
3.0601-3.50260.26422200.20133787X-RAY DIFFRACTION98
3.5026-4.41180.21042020.15783855X-RAY DIFFRACTION99
4.4118-37.29580.19641990.15743984X-RAY DIFFRACTION97
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)
12.113-1.47190.82592.8963-0.6871.06940.00540.11790.2141-0.1603-0.0786-0.31460.02520.1090.06220.1002-0.016-0.01780.12780.00450.1561-0.817639.04663.3912
21.69-0.29640.96391.4763-0.71662.53070.012-0.13170.0474-0.01620.12450.22550.0863-0.1926-0.10750.1228-0.0345-0.00620.1387-0.00950.1889-17.331244.169414.6785
33.4206-0.5371-1.78411.9288-0.77070.78380.1255-0.57170.3623-0.4085-0.2543-0.1340.09660.3060.10170.2706-0.0067-0.02850.3729-0.01580.208220.443749.806126.7554
42.0140.06892.53620.4435-0.68542.91010.1253-0.006-0.0427-0.0126-0.15790.0060.08520.05230.03150.1936-0.0256-0.05050.26490.00380.109119.624431.799835.9846
52.01490.63790.65732.77370.7270.7690.1756-0.3616-0.47320.323-0.3187-0.05140.3903-0.07120.02820.173-0.0709-0.06140.18790.15540.3109-3.969712.853320.7691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA151 - 253
2X-RAY DIFFRACTION2chain BB151 - 253
3X-RAY DIFFRACTION3chain CC152 - 253
4X-RAY DIFFRACTION4chain DD151 - 245
5X-RAY DIFFRACTION5chain EE151 - 247

+
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