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- PDB-3eul: Structure of the signal receiver domain of the putative response ... -

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Basic information

Entry
Database: PDB / ID: 3eul
TitleStructure of the signal receiver domain of the putative response regulator NarL from Mycobacterium tuberculosis
ComponentsPOSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)
KeywordsTRANSCRIPTION / Central beta strand flanked by alpha helices / DNA-binding / Transcription regulation
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / 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 ...LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable transcriptional regulatory protein NarL / Probable transcriptional regulatory protein NarL
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchneider, G. / Schnell, R. / Agren, D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: 1.9 A structure of the signal receiver domain of the putative response regulator NarL from Mycobacterium tuberculosis.
Authors: Schnell, R. / Agren, D. / Schneider, G.
History
DepositionOct 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 6, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)
B: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)
C: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)
D: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8945
Polymers64,8584
Non-polymers351
Water3,135174
1
A: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)


Theoretical massNumber of molelcules
Total (without water)16,2151
Polymers16,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2502
Polymers16,2151
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)


Theoretical massNumber of molelcules
Total (without water)16,2151
Polymers16,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)


Theoretical massNumber of molelcules
Total (without water)16,2151
Polymers16,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)
D: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)


Theoretical massNumber of molelcules
Total (without water)32,4292
Polymers32,4292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-13 kcal/mol
Surface area10050 Å2
MethodPISA
6
B: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)
C: POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4653
Polymers32,4292
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-11 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.532, 90.038, 126.336
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL (DNA-binding response regulator, LuxR family)


Mass: 16214.541 Da / Num. of mol.: 4 / Fragment: Signal receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0866, narL, Rv0844c / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: O53856, UniProt: P9WGM5*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 1.88 Å3/Da / Density % sol: 34.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Tris-HCl pH 8.5, 0.2M KBr, 26% PEG 2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.904922 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 2005
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.904922 Å / Relative weight: 1
ReflectionResolution: 1.9→63.1 Å / Num. obs: 38512 / % possible obs: 100 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Rsym value: 0.077
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.0451 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B2N

3b2n


Resolution: 1.9→45 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.569 / SU ML: 0.126 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26989 1941 5 %RANDOM
Rwork0.21727 ---
obs0.21988 36779 99.92 %-
all-38759 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.075 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--1.31 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 1 174 3443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223309
X-RAY DIFFRACTIONr_bond_other_d0.0020.022187
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9864487
X-RAY DIFFRACTIONr_angle_other_deg1.07835354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22823.852135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82315548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4691527
X-RAY DIFFRACTIONr_chiral_restr0.1260.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02625
X-RAY DIFFRACTIONr_nbd_refined0.2130.2743
X-RAY DIFFRACTIONr_nbd_other0.1950.22283
X-RAY DIFFRACTIONr_nbtor_refined0.170.21617
X-RAY DIFFRACTIONr_nbtor_other0.0870.21858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0361.52792
X-RAY DIFFRACTIONr_mcbond_other0.1841.5893
X-RAY DIFFRACTIONr_mcangle_it1.19423464
X-RAY DIFFRACTIONr_scbond_it2.04231237
X-RAY DIFFRACTIONr_scangle_it3.0934.51023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 149 -
Rwork0.297 2685 -
obs--100 %

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