[English] 日本語
Yorodumi
- PDB-1zg5: NarL complexed to narG-89 promoter palindromic tail-to-tail DNA site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zg5
TitleNarL complexed to narG-89 promoter palindromic tail-to-tail DNA site
Components
  • 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP*G)-3'
  • Nitrate/nitrite response regulator protein narL
KeywordsTRANSCRIPTION/DNA / protein-DNA complex / helix-turn-helix / two-component response regulator / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMaris, A.E. / Kaczor-Grzeskowiak, M. / Ma, Z. / Kopka, M.L. / Gunsalus, R.P. / Dickerson, R.E.
Citation
Journal: Biochemistry / Year: 2005
Title: Primary and Secondary Modes of DNA Recognition by the NarL Two-Component Response Regulator.
Authors: Maris, A.E. / Kaczor-Grzeskowiak, M. / Ma, Z. / Kopka, M.L. / Gunsalus, R.P. / Dickerson, R.E.
#1: Journal: 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.D. / Kopka, M.L. / Schroeder, I. / Gunsalus, R.P. / Dickerson, R.E.
#2: Journal: Biochemistry / Year: 1996
Title: Structure of the Escherichia coli response regulator NarL
Authors: Baikalov, I. / Schroeder, I. / Kaczor-Grzeskowiak, M. / Grzeskowiak, K. / Gunsalus, R.P. / Dickerson, R.E.
History
DepositionApr 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP*G)-3'
G: 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP*G)-3'
H: 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*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)65,00420
Polymers63,8528
Non-polymers1,15312
Water4,684260
1
C: 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*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)32,50210
Polymers31,9264
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*GP*GP*GP*TP*AP*CP*G)-3'
H: 5'-D(*CP*GP*TP*AP*CP*CP*CP*CP*TP*AP*TP*AP*GP*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)32,50210
Polymers31,9264
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.890, 52.570, 84.610
Angle α, β, γ (deg.)90.00, 89.995, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer bound to DNA. There are two biological units in the asymmetric unit (chains A, B, C & D and chains E, F, G & H)

-
Components

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


Mass: 6134.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: solid phase synthesis
#2: Protein
Nitrate/nitrite response regulator protein narL


Mass: 9827.909 Da / Num. of mol.: 4 / Fragment: DNA binding domain (residues 147-216)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NARL / Plasmid: pMJ05 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0AF28
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, pH 7.5, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 34483 / Num. obs: 34483 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 52.2 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.131 / Χ2: 1.948 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.25 Å / % possible obs: 96.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.9 / Num. measured obs: 2194 / Num. unique all: 2194 / Rsym value: 0.954 / Χ2: 4.303 / % possible all: 96.4

-
Processing

Software
NameClassificationNB
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JE8

1je8


Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1495 4.9 %random
Rwork0.219 ---
all-30200 --
obs-30200 99.5 %-
Solvent computationBsol: 38.791 Å2
Displacement parametersBiso mean: 40.426 Å2
Baniso -1Baniso -2Baniso -3
1-1.839 Å20 Å20 Å2
2--7.065 Å20 Å2
3----8.905 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 1628 60 260 4149
Refine LS restraints
Refine-IDTypeDev idealWeightDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1871.5
X-RAY DIFFRACTIONc_scbond_it1.84420
X-RAY DIFFRACTIONc_mcangle_it2.03620
X-RAY DIFFRACTIONc_scangle_it2.912.50
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.384 230 -
Rwork0.333 --
obs--99.4 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

+
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