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- PDB-1zg1: NarL complexed to nirB promoter non-palindromic tail-to-tail DNA site -

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Basic information

Entry
Database: PDB / ID: 1zg1
TitleNarL complexed to nirB promoter non-palindromic tail-to-tail DNA site
Components
  • 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*GP*GP*AP*GP*TP*AP*CP*G)-3'
  • 5'-D(*CP*GP*TP*AP*CP*TP*CP*CP*TP*TP*AP*AP*TP*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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*CP*GP*TP*AP*CP*TP*CP*CP*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*GP*GP*AP*GP*TP*AP*CP*G)-3'
G: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*GP*GP*AP*GP*TP*AP*CP*G)-3'
H: 5'-D(*CP*GP*TP*AP*CP*TP*CP*CP*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)64,71217
Polymers63,8488
Non-polymers8659
Water1,60389
1
C: 5'-D(*CP*GP*TP*AP*CP*TP*CP*CP*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*GP*GP*AP*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)32,4049
Polymers31,9244
Non-polymers4805
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*GP*GP*AP*GP*TP*AP*CP*G)-3'
H: 5'-D(*CP*GP*TP*AP*CP*TP*CP*CP*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)76.580, 52.820, 84.970
Angle α, β, γ (deg.)90.00, 90.07, 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)

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Components

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


Mass: 6124.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid phase synthesis
#2: DNA chain 5'-D(*CP*GP*TP*AP*CP*CP*CP*AP*TP*TP*AP*AP*GP*GP*AP*GP*TP*AP*CP*G)-3'


Mass: 6142.993 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid phase synthesis
#3: 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, frdR / Plasmid: pMJ05 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0AF28
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium sulfate, pH 7.5, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium sulfate11
2H2O11
3Ammonium sulfate12
4H2O12

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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: 2.25→25 Å / Num. all: 32539 / Num. obs: 32539 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.067 / Χ2: 0.989 / Net I/σ(I): 18.3
Reflection shellResolution: 2.25→2.3 Å / % possible obs: 98.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.9 / Num. measured obs: 1942 / Num. unique all: 1942 / Rsym value: 0.469 / Χ2: 1.047 / % possible all: 98.8

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Processing

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

1je8


Resolution: 2.3→9 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1490 5 %random
Rwork0.257 ---
all-29453 --
obs-29453 98.3 %-
Solvent computationBsol: 45.36 Å2
Displacement parametersBiso mean: 45.475 Å2
Baniso -1Baniso -2Baniso -3
1-11.478 Å20 Å20.139 Å2
2--17.576 Å20 Å2
3----29.054 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.3→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 1628 45 89 3954
Refine LS restraints
Refine-IDTypeDev idealWeightDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2831.5
X-RAY DIFFRACTIONc_scbond_it1.96420
X-RAY DIFFRACTIONc_mcangle_it2.04420
X-RAY DIFFRACTIONc_scangle_it2.8842.50
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.402 231 -
Rwork0.369 --
obs--99.1 %
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

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