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- PDB-1a04: THE STRUCTURE OF THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN N... -

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Basic information

Entry
Database: PDB / ID: 1a04
TitleTHE STRUCTURE OF THE NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL IN THE MONOCLINIC C2 CRYSTAL FORM
ComponentsNITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL
KeywordsSIGNAL TRANSDUCTION PROTEIN / RESPONSE REGULATORS / TWO-COMPONENT SYSTEMS
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 / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Nitrate/nitrite response regulator protein NarL / Nitrate/nitrite response regulator protein NarL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBaikalov, I. / Schroder, I. / Kaczor-Grzeskowiak, M. / Cascio, D. / Gunsalus, R.P. / Dickerson, R.E.
Citation
Journal: Biochemistry / Year: 1998
Title: NarL dimerization? Suggestive evidence from a new crystal form
Authors: Baikalov, I. / Schroder, I. / Kaczor-Grzeskowiak, M. / Cascio, D. / Gunsalus, R.P. / Dickerson, R.E.
#1: Journal: Biochemistry / Year: 1996
Title: Structure of the Escherichia Coli Response Regulator NarL.
Authors: Baikalov, I. / Schroder, I. / Kaczor-Grzeskowiak, M. / Grzeskowiak, K. / Gunsalus, R.P. / Dickerson, R.E.
History
DepositionDec 8, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL
B: NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL


Theoretical massNumber of molelcules
Total (without water)47,6572
Polymers47,6572
Non-polymers00
Water6,503361
1
A: NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL


Theoretical massNumber of molelcules
Total (without water)23,8291
Polymers23,8291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL


Theoretical massNumber of molelcules
Total (without water)23,8291
Polymers23,8291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.306, 38.527, 106.892
Angle α, β, γ (deg.)90.00, 131.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL


Mass: 23828.623 Da / Num. of mol.: 2 / Fragment: RESIDUES 2 - 216 OF THE WILD TYPE NARL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Plasmid: PHXL-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P10957, UniProt: P0AF28*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: THE PROTEIN SOLUTION CONTAINING 23.3 MG/ML OF PURIFIED NARL, 20 MM TRIS.HCL (PH=7.6), 0.5 MM MGCL2, AND 10% GLYCEROL WAS MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 0.1 M ...Details: THE PROTEIN SOLUTION CONTAINING 23.3 MG/ML OF PURIFIED NARL, 20 MM TRIS.HCL (PH=7.6), 0.5 MM MGCL2, AND 10% GLYCEROL WAS MIXED WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 0.1 M TRIS.HCL (PH=8.5), 0.2 M SODIUM ACETATE, AND 30% POLYETHYLENE GLYCOL (PEG) 4000. SITTING DROPS CONTAINING 20 ML OF MIXTURE WERE EQUILIBRATED BY VAPOR DIFFUSION AT 4 DEGREES AGAINST 20 ML OF THE RESERVOIR SOLUTION. CRYSTALS BEGAN TO APPEAR AS CLUSTERS OF PLATES AFTER 11-15 DAYS., vapor diffusion - sitting drop, temperature 277K
PH range: 7.6-8.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111.65 mg/mlNarL1drop
210 mMTris-HCl1drop
30.25 mM1dropMgCl2
45 %glycerol1drop
50.05 MTris-HCl1drop
60.1 Msodium acetate1drop
715 %PEG40001drop
80.1 MTris-HCl1reservoir
90.2 Msodium acetate1reservoir
1030 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 27, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→65 Å / Num. obs: 22871 / % possible obs: 99.87 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 9.8
Reflection shellResolution: 2.2→2.44 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RNL

1rnl


Resolution: 2.2→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 -10 %RANDOM
Rwork0.211 ---
obs0.211 22321 99 %-
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 0 361 3535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.36
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2

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