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- PDB-1je8: Two-Component response regulator NarL/DNA Complex: DNA Bending Fo... -

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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

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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*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

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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

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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: 2.65 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

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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

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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

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