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- PDB-1zlk: Crystal Structure of the Mycobacterium tuberculosis Hypoxic Respo... -

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Basic information

Entry
Database: PDB / ID: 1zlk
TitleCrystal Structure of the Mycobacterium tuberculosis Hypoxic Response Regulator DosR C-terminal Domain-DNA Complex
Components
  • 5'-D(*CP*GP*TP*GP*GP*CP*CP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*AP*CP*TP*TP*TP*AP*GP*TP*CP*CP*CP*CP*AP*AP*AP*GP*CP*GP*CP*GP*GP*GP*CP*CP*AP*T)-3'
  • 5'-D(*GP*GP*CP*CP*CP*GP*CP*GP*CP*TP*TP*TP*GP*GP*GP*GP*AP*CP*TP*AP*AP*AP*GP*TP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*GP*GP*CP*CP*AP*CP*GP*AP*T)-3'
  • Dormancy Survival Regulator
KeywordsTranscription/DNA / helix-turn-helix / protein-DNA complex / Transcription-DNA COMPLEX
Function / homology
Function and homology information


host cell endosome lumen / dormancy process / host cell cytoplasmic vesicle / phosphorelay signal transduction system / peptidoglycan-based cell wall / response to hypoxia / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding / extracellular space ...host cell endosome lumen / dormancy process / host cell cytoplasmic vesicle / phosphorelay signal transduction system / peptidoglycan-based cell wall / response to hypoxia / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding / extracellular space / plasma membrane / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA-binding transcriptional activator DevR/DosR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWisedchaisri, G. / Wu, M. / Rice, A.E. / Roberts, D.M. / Sherman, D.R. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structures of Mycobacterium tuberculosis DosR and DosR-DNA complex involved in gene activation during adaptation to hypoxic latency.
Authors: Wisedchaisri, G. / Wu, M. / Rice, A.E. / Roberts, D.M. / Sherman, D.R. / Hol, W.G.J.
History
DepositionMay 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*GP*CP*CP*CP*GP*CP*GP*CP*TP*TP*TP*GP*GP*GP*GP*AP*CP*TP*AP*AP*AP*GP*TP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*GP*GP*CP*CP*AP*CP*GP*AP*T)-3'
D: 5'-D(*CP*GP*TP*GP*GP*CP*CP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*AP*CP*TP*TP*TP*AP*GP*TP*CP*CP*CP*CP*AP*AP*AP*GP*CP*GP*CP*GP*GP*GP*CP*CP*AP*T)-3'
A: Dormancy Survival Regulator
B: Dormancy Survival Regulator


Theoretical massNumber of molelcules
Total (without water)47,5134
Polymers47,5134
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.397, 58.791, 82.933
Angle α, β, γ (deg.)90.00, 125.50, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPARGARG2AC145 - 20923 - 87
211ASPASPARGARG2BD145 - 20923 - 87
112DGDGDTDT4CA14 - 1914 - 19
212DGDGDTDT4DB14 - 1915 - 20
322DADADCDC4CA22 - 2722 - 27
422DADADCDC4DB22 - 2723 - 28

NCS ensembles :
ID
1
2
DetailsThe asymmetric unit contains 2 biological protein monomers forming one functional dimer bound to double-stranded oligonucleotide.

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Components

#1: DNA chain 5'-D(*GP*GP*CP*CP*CP*GP*CP*GP*CP*TP*TP*TP*GP*GP*GP*GP*AP*CP*TP*AP*AP*AP*GP*TP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*GP*GP*CP*CP*AP*CP*GP*AP*T)-3'


Mass: 13182.437 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*TP*GP*GP*CP*CP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*AP*CP*TP*TP*TP*AP*GP*TP*CP*CP*CP*CP*AP*AP*AP*GP*CP*GP*CP*GP*GP*GP*CP*CP*AP*T)-3'


Mass: 13302.508 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Dormancy Survival Regulator / DosR


Mass: 10513.998 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dosR, devR, Rv3133c / Plasmid: pET28(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 15610269, UniProt: P9WMF9*PLUS

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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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 400, HEPES, calcium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2HEPES11
3calcium chloride11
4H2O11
5PEG 40012
6HEPES12
7calcium chloride12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.96411 Å
DetectorDetector: CCD / Date: Mar 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96411 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 8211 / % possible obs: 79.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 72.8 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.7
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.03 / % possible all: 60.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZLJ

1zlj


Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.865 / SU B: 23.638 / SU ML: 0.394 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.996 / ESU R Free: 0.499 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28802 407 5 %RANDOM
Rwork0.27154 ---
all0.27233 7800 --
obs0.27233 7800 79.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 82.903 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å22.86 Å2
2---4 Å20 Å2
3---8.37 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1010 1008 0 0 2018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212148
X-RAY DIFFRACTIONr_bond_other_d0.0010.021471
X-RAY DIFFRACTIONr_angle_refined_deg1.0862.5653104
X-RAY DIFFRACTIONr_angle_other_deg0.84133503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2425128
X-RAY DIFFRACTIONr_chiral_restr0.0480.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02206
X-RAY DIFFRACTIONr_nbd_refined0.220.3524
X-RAY DIFFRACTIONr_nbd_other0.2580.31961
X-RAY DIFFRACTIONr_nbtor_other0.0880.51001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.567
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.37
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.51
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11C384tight positional0.050.1
11C619medium positional0.190.4
22A360medium positional0.140.4
LS refinement shellResolution: 3.1→3.183 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.569 15
Rwork0.427 385

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