[English] 日本語
Yorodumi
- PDB-1je8: Two-Component response regulator NarL/DNA Complex: DNA Bending Fo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1je8
TitleTwo-Component response regulator NarL/DNA Complex: DNA Bending Found in a High Affinity Site
Components
  • 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'
  • Nitrate/Nitrite Response Regulator Protein NARL
KeywordsTRANSCRIPTION/DNA / Protein-DNA complex / Two-Component response regulator / helix-turn-helix / DNA bending / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription repressor activity / phosphorelay signal transduction system / nitrate assimilation / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / DNA binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Nitrate/nitrite response regulator protein NarL / Nitrate/nitrite response regulator protein NarL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsMaris, A.E. / Sawaya, M.R. / Kaczor-Grzeskowiak, M. / Jarvis, M.R. / Bearson, S.M.D. / Kopka, M.L. / Schroder, I. / Gunsalus, R.P. / Dickerson, R.E.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Dimerization allows DNA target site recognition by the NarL response regulator.
Authors: Maris, A.E. / Sawaya, M.R. / Kaczor-Grzeskowiak, M. / Jarvis, M.R. / Bearson, S.M. / Kopka, M.L. / Schroder, I. / Gunsalus, R.P. / Dickerson, R.E.
History
DepositionJun 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'
G: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'
H: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'
A: Nitrate/Nitrite Response Regulator Protein NARL
B: Nitrate/Nitrite Response Regulator Protein NARL
E: Nitrate/Nitrite Response Regulator Protein NARL
F: Nitrate/Nitrite Response Regulator Protein NARL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,61616
Polymers63,8488
Non-polymers7698
Water5,945330
1
C: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'
A: Nitrate/Nitrite Response Regulator Protein NARL
B: Nitrate/Nitrite Response Regulator Protein NARL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3088
Polymers31,9244
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'
H: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'
E: Nitrate/Nitrite Response Regulator Protein NARL
F: Nitrate/Nitrite Response Regulator Protein NARL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3088
Polymers31,9244
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.257, 52.741, 83.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: DNA chain
5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*TP*GP*GP*GP*TP*AP*CP*G)-3'


Mass: 6133.979 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: DNA was synthesized using solid phase phosphoramidite chemistry.
#2: Protein
Nitrate/Nitrite Response Regulator Protein NARL


Mass: 9827.909 Da / Num. of mol.: 4 / Fragment: DNA Binding Domain (147-216)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pMJ05 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P10957, UniProt: P0AF28*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulfate11
2TRIS11
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13.5 mg/mlNarL1drop
21.3 mg/mlDNA1drop
30.04 M1dropKCl
40.1 %(v/v)glycerol1drop
50.1 mM1dropMgCl2
610 mMTris1droppH7.5
70.7 Mammonium sulfate1drop
81.7 Mammonium sulfate1reservoir
90.1 MTris1reservoirpH7.5
105 mMbeta-mercaptoethanol1reservoir

-
Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.10002 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2000
Details: Collimating mirror optics, double slit monochromator
RadiationMonochromator: SI 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.10002 Å / Relative weight: 1
ReflectionResolution: 2.13→100 Å / Num. all: 69333 / Num. obs: 69333 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 21.5 Å2 / Rsym value: 0.048 / Net I/σ(I): 19.1
Reflection shellResolution: 2.13→2.18 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 3610 / Rsym value: 0.194 / % possible all: 73.3
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 100 Å / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 73.3 % / Rmerge(I) obs: 0.194

-
Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
GLRFphasing
CNS1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DNA-Binding Domain of 1RNL bound to DNA

1rnl


Resolution: 2.12→8.97 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Data collection, processing and initial refinement was in P1. Final refinement was in P21. The model used for MR was built from MAD phasing results from a similar crystal.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1797 5 %random
Rwork0.228 ---
all-36074 --
obs-36074 96.2 %-
Solvent computationSolvent model: flat model / Bsol: 75.9 Å2 / ksol: 0.489 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1--8.32 Å20 Å20 Å2
2---10.24 Å20 Å2
3---18.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.12→8.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 1628 40 330 4199
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.058
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it1.276
X-RAY DIFFRACTIONc_mcangle_it1.982
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.564
LS refinement shellResolution: 2.12→2.25 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 264 4.9 %
Rwork0.314 5163 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna_nodihe.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Lowest resolution: 9 Å / Num. reflection obs: 34277 / % reflection Rfree: 5 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04
LS refinement shell
*PLUS
Rfactor Rfree: 0.324 / Rfactor Rwork: 0.314

+
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