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- PDB-3c57: Crystal Structure of the Mycobacterium tuberculosis Hypoxic Respo... -

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Basic information

Entry
Database: PDB / ID: 3c57
TitleCrystal Structure of the Mycobacterium tuberculosis Hypoxic Response Regulator DosR C-terminal Domain Crystal Form II
ComponentsTWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR
KeywordsTRANSCRIPTION / RESPONSE REGULATOR / TWO-COMPONENT REGULATORY SYSTEM / DNA-BINDING PROTEIN / TUBERCULOSIS / TRANSCRIPTION REGULATION
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 / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding ...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 / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / extracellular space / plasma membrane / cytosol / cytoplasm
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-binding transcriptional activator DevR/DosR / DNA-binding transcriptional activator DevR/DosR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWisedchaisri, G. / Wu, M. / Sherman, D.R. / Hol, W.G.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of the response regulator DosR from Mycobacterium tuberculosis suggest a helix rearrangement mechanism for phosphorylation activation
Authors: Wisedchaisri, G. / Wu, M. / Sherman, D.R. / Hol, W.G.
History
DepositionJan 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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

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Assembly

Deposited unit
A: TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR
B: TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR


Theoretical massNumber of molelcules
Total (without water)21,0282
Polymers21,0282
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR


Theoretical massNumber of molelcules
Total (without water)10,5141
Polymers10,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR


Theoretical massNumber of molelcules
Total (without water)10,5141
Polymers10,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.637, 47.400, 66.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 6 / Auth seq-ID: 151 - 199 / Label seq-ID: 29 - 77

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR / PROBABLY LUXR/UHPA-FAMILY / DevR / DNA-binding response regulator / LuxR family


Mass: 10513.998 Da / Num. of mol.: 2 / Fragment: C-terminal Domain residues 144-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: devR / Plasmid: pET-28(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P95193, UniProt: P9WMF9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 24% w/v PEG 5000mme, 0.2M ammonium sulfate, 10% glycerol, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 14128 / % possible obs: 98.5 % / Redundancy: 6.43 % / Rsym value: 0.091 / Net I/σ(I): 19.3
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.59

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DosR C-terminal domain (pdb code 1ZLJ) subunit A residues 152-192

1zlj


Resolution: 1.7→38.58 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.674 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic and TLS / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20612 704 5 %RANDOM
Rwork0.1885 ---
obs0.1894 14088 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms768 0 0 49 817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022832
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.332.0171130
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8885119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.89522.532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08615178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4881510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02588
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.3337
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.5585
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.576
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.382
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.518
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.094547
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6315846
X-RAY DIFFRACTIONr_scbond_it3.7915318
X-RAY DIFFRACTIONr_scangle_it5.1436273
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 355 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.485
loose thermal1.4510
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 41 -
Rwork0.236 899 -
obs-940 90.38 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.46480.24514.737733.62192.798311.77040.1685-0.14410.1172-0.0748-0.0448-0.1050.1550.0542-0.12380.0235-0.04720.04570.1526-0.01220.062643.25114.63227.556
212.1151-5.3981.79086.45870.893410.41440.02080.5343-0.06610.2677-0.14840.21150.10530.06140.1277-0.0103-0.01560.00130.09270.00050.053348.77816.9224.646
317.09057.44546.40227.95543.03087.234-0.0727-0.1517-0.0276-0.10080.04010.1682-0.05990.1320.0326-0.00930.03280.01670.0851-0.01560.070350.52410.75921.709
432.39749.45196.239811.8784.98047.0150.1478-0.26010.0913-0.0544-0.23490.14870.2618-0.05230.0870.0621-0.0015-0.02040.0328-0.00770.090239.6674.86318.954
54.9871.21212.13519.03765.62511.76660.0964-0.0387-0.01440.09190.1897-0.2009-0.0760.0712-0.2861-0.00760.0158-0.00920.0677-0.02170.09635.377-2.55715.693
69.48465.4269-1.558417.30652.51535.25460.1420.1028-0.06560.0732-0.0308-0.0856-0.25670.0253-0.11120.0739-0.02280.01360.1318-0.01240.05630.9623.70122.168
715.9274-5.0322-1.49719.0911-2.72797.42920.24640.3128-0.05620.1406-0.3540.0921-0.0590.35230.10760.0126-0.01950.01730.1237-0.04080.113226.9011.85519.432
818.55759.36921.82411.98482.44535.1688-0.0108-0.047-0.32770.0238-0.0445-0.2306-0.1755-0.1390.0553-0.00740.0154-0.00540.0773-0.00850.119329.1588.18917.16
933.347316.80172.674610.90492.31466.27970.21070.0619-0.1980.0627-0.1863-0.0995-0.1355-0.142-0.02440.0222-0.0039-0.00010.04020.00860.106937.27813.93518.313
1010.20113.361-2.452918.47-4.12478.09830.1843-0.10740.0462-0.1381-0.0855-0.0030.06750.0233-0.0988-0.00910.0057-0.02580.06560.03420.093843.90421.51217.682
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA149 - 16427 - 42
2X-RAY DIFFRACTION2AA165 - 17743 - 55
3X-RAY DIFFRACTION3AA178 - 18656 - 64
4X-RAY DIFFRACTION4AA187 - 19365 - 71
5X-RAY DIFFRACTION5AA194 - 19972 - 77
6X-RAY DIFFRACTION6BB151 - 16629 - 44
7X-RAY DIFFRACTION7BB167 - 17645 - 54
8X-RAY DIFFRACTION8BB177 - 18655 - 64
9X-RAY DIFFRACTION9BB187 - 19365 - 71
10X-RAY DIFFRACTION10BB194 - 19972 - 77

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