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- PDB-5wm9: Crystal Structure of TetR family regulator Rv0078 from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 5wm9
TitleCrystal Structure of TetR family regulator Rv0078 from Mycobacterium tuberculosis
ComponentsRv0078
KeywordsTRANSCRIPTION / Mycobacterium tuberculosis / Rv0078 / TetR
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / plasma membrane
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain / : / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
Probable transcriptional regulatory protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85000290276 Å
AuthorsHsu, H.C. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI070285 United States
CitationJournal: MBio / Year: 2018
Title: Cytokinin Signaling in Mycobacterium tuberculosis.
Authors: Samanovic, M.I. / Hsu, H.C. / Jones, M.B. / Jones, V. / McNeil, M.R. / Becker, S.H. / Jordan, A.T. / Strnad, M. / Xu, C. / Jackson, M. / Li, H. / Darwin, K.H.
History
DepositionJul 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rv0078
B: Rv0078
C: Rv0078
D: Rv0078
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2007
Polymers93,9124
Non-polymers2883
Water8,053447
1
A: Rv0078
D: Rv0078
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0523
Polymers46,9562
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-37 kcal/mol
Surface area18630 Å2
MethodPISA
2
B: Rv0078
C: Rv0078
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1484
Polymers46,9562
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-49 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.909, 67.075, 56.016
Angle α, β, γ (deg.)90.000, 99.187, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 7 or resseq 10 or resseq...A7
121(chain A and (resseq 7 or resseq 10 or resseq...A10
131(chain A and (resseq 7 or resseq 10 or resseq...A12 - 16
141(chain A and (resseq 7 or resseq 10 or resseq...A18 - 29
151(chain A and (resseq 7 or resseq 10 or resseq...A31 - 51
161(chain A and (resseq 7 or resseq 10 or resseq...A53 - 62
171(chain A and (resseq 7 or resseq 10 or resseq...A64 - 70
181(chain A and (resseq 7 or resseq 10 or resseq...A72 - 73
191(chain A and (resseq 7 or resseq 10 or resseq...A75 - 109
1101(chain A and (resseq 7 or resseq 10 or resseq...A111 - 129
1111(chain A and (resseq 7 or resseq 10 or resseq...A134 - 135
1121(chain A and (resseq 7 or resseq 10 or resseq...A138 - 146
1131(chain A and (resseq 7 or resseq 10 or resseq...A148 - 151
1141(chain A and (resseq 7 or resseq 10 or resseq...A154 - 176
1151(chain A and (resseq 7 or resseq 10 or resseq...A179 - 180
1161(chain A and (resseq 7 or resseq 10 or resseq...A183 - 184
1171(chain A and (resseq 7 or resseq 10 or resseq...A186 - 187
1181(chain A and (resseq 7 or resseq 10 or resseq...A189 - 191
1191(chain A and (resseq 7 or resseq 10 or resseq...A193 - 199
211(chain B and (resseq 7 or resseq 10 or resseq...B7
221(chain B and (resseq 7 or resseq 10 or resseq...B10
231(chain B and (resseq 7 or resseq 10 or resseq...B12 - 16
241(chain B and (resseq 7 or resseq 10 or resseq...B18 - 29
251(chain B and (resseq 7 or resseq 10 or resseq...B31 - 51
261(chain B and (resseq 7 or resseq 10 or resseq...B53 - 62
271(chain B and (resseq 7 or resseq 10 or resseq...B64 - 70
281(chain B and (resseq 7 or resseq 10 or resseq...B72 - 73
291(chain B and (resseq 7 or resseq 10 or resseq...B75 - 109
2101(chain B and (resseq 7 or resseq 10 or resseq...B111 - 129
2111(chain B and (resseq 7 or resseq 10 or resseq...B134 - 135
2121(chain B and (resseq 7 or resseq 10 or resseq...B138 - 146
2131(chain B and (resseq 7 or resseq 10 or resseq...B148 - 151
2141(chain B and (resseq 7 or resseq 10 or resseq...B154 - 176
2151(chain B and (resseq 7 or resseq 10 or resseq...B179 - 180
2161(chain B and (resseq 7 or resseq 10 or resseq...B183 - 184
2171(chain B and (resseq 7 or resseq 10 or resseq...B186 - 187
2181(chain B and (resseq 7 or resseq 10 or resseq...B189 - 191
2191(chain B and (resseq 7 or resseq 10 or resseq...B193 - 199
311(chain C and (resseq 7 or resseq 10 or resseq...C7
321(chain C and (resseq 7 or resseq 10 or resseq...C10
331(chain C and (resseq 7 or resseq 10 or resseq...C12 - 16
341(chain C and (resseq 7 or resseq 10 or resseq...C18 - 29
351(chain C and (resseq 7 or resseq 10 or resseq...C31 - 51
361(chain C and (resseq 7 or resseq 10 or resseq...C53 - 62
371(chain C and (resseq 7 or resseq 10 or resseq...C64 - 70
381(chain C and (resseq 7 or resseq 10 or resseq...C72 - 73
391(chain C and (resseq 7 or resseq 10 or resseq...C75 - 109
3101(chain C and (resseq 7 or resseq 10 or resseq...C111 - 129
3111(chain C and (resseq 7 or resseq 10 or resseq...C134 - 135
3121(chain C and (resseq 7 or resseq 10 or resseq...C138 - 146
3131(chain C and (resseq 7 or resseq 10 or resseq...C148 - 151
3141(chain C and (resseq 7 or resseq 10 or resseq...C154 - 176
3151(chain C and (resseq 7 or resseq 10 or resseq...C179 - 180
3161(chain C and (resseq 7 or resseq 10 or resseq...C183 - 184
3171(chain C and (resseq 7 or resseq 10 or resseq...C186 - 187
3181(chain C and (resseq 7 or resseq 10 or resseq...C189 - 191
3191(chain C and (resseq 7 or resseq 10 or resseq...C193 - 199
411(chain D and (resseq 7 or resseq 10 or resseq...D7
421(chain D and (resseq 7 or resseq 10 or resseq...D10
431(chain D and (resseq 7 or resseq 10 or resseq...D12 - 16
441(chain D and (resseq 7 or resseq 10 or resseq...D18 - 29
451(chain D and (resseq 7 or resseq 10 or resseq...D31 - 51
461(chain D and (resseq 7 or resseq 10 or resseq...D53 - 62
471(chain D and (resseq 7 or resseq 10 or resseq...D64 - 70
481(chain D and (resseq 7 or resseq 10 or resseq...D72 - 73
491(chain D and (resseq 7 or resseq 10 or resseq...D75 - 109
4101(chain D and (resseq 7 or resseq 10 or resseq...D111 - 129
4111(chain D and (resseq 7 or resseq 10 or resseq...D134 - 135
4121(chain D and (resseq 7 or resseq 10 or resseq...D138 - 146
4131(chain D and (resseq 7 or resseq 10 or resseq...D148 - 151
4141(chain D and (resseq 7 or resseq 10 or resseq...D154 - 176
4151(chain D and (resseq 7 or resseq 10 or resseq...D179 - 180
4161(chain D and (resseq 7 or resseq 10 or resseq...D183 - 184
4171(chain D and (resseq 7 or resseq 10 or resseq...D186 - 187
4181(chain D and (resseq 7 or resseq 10 or resseq...D189 - 191
4191(chain D and (resseq 7 or resseq 10 or resseq...D193 - 199

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Components

#1: Protein
Rv0078 / transcriptional regulatory protein


Mass: 23477.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv0078 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O53623
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.1 M sodium cacodylate, pH 6.4, 1.3 M lithium sulfate
PH range: 6.4-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 21, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.85→111.01 Å / Num. obs: 67749 / % possible obs: 96.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 22.6440283861 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.031 / Net I/σ(I): 16.9
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3 / Num. unique obs: 9693 / CC1/2: 0.88 / Rpim(I) all: 0.261 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIXrefinement
PHENIX1.10.1_2155phasing
PHENIX1.10.1_2155model building
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85000290276→36.3782148197 Å / SU ML: 0.227919634992 / Cross valid method: FREE R-VALUE / σ(F): 1.3378407559 / Phase error: 24.7458719766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.240324718465 3427 5.0604686877 %
Rwork0.207406524933 64294 -
obs0.209026281237 67721 96.1618198341 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.6814423048 Å2
Refinement stepCycle: LAST / Resolution: 1.85000290276→36.3782148197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5925 0 15 447 6387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005098125467746017
X-RAY DIFFRACTIONf_angle_d0.6716294580028159
X-RAY DIFFRACTIONf_chiral_restr0.0436333001873947
X-RAY DIFFRACTIONf_plane_restr0.005512637224451073
X-RAY DIFFRACTIONf_dihedral_angle_d17.99195345073677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87640.3058682320361470.2835959810972609X-RAY DIFFRACTION94.4158958547
1.8764-1.90440.3053295197291140.2655447646232658X-RAY DIFFRACTION94.9315068493
1.9044-1.93420.287589303711640.2524903031682618X-RAY DIFFRACTION94.6258503401
1.9342-1.96590.3168084317781360.2386724455742641X-RAY DIFFRACTION95.7916522939
1.9659-1.99980.2639570917871460.2297236540862636X-RAY DIFFRACTION95.2413557001
1.9998-2.03620.2496899270811550.2231769915252661X-RAY DIFFRACTION96.0109103307
2.0362-2.07530.2923720120611470.2282379525272639X-RAY DIFFRACTION95.5746140652
2.0753-2.11770.2781103818141410.2250094766612633X-RAY DIFFRACTION96.2526023595
2.1177-2.16370.2860325891851390.225341642842685X-RAY DIFFRACTION95.9891230455
2.1637-2.2140.2802053436221310.2184352674432678X-RAY DIFFRACTION96.529209622
2.214-2.26940.2572128766431380.2189793171132644X-RAY DIFFRACTION95.8979662185
2.2694-2.33080.2749418350581460.2149300933992702X-RAY DIFFRACTION96.3464140731
2.3308-2.39930.2318006976931520.213413066382669X-RAY DIFFRACTION96.941580756
2.3993-2.47680.2618309863061670.2118789735652660X-RAY DIFFRACTION96.7819239986
2.4768-2.56530.2132994492911370.2120434678782723X-RAY DIFFRACTION96.9162995595
2.5653-2.66790.2905197101111300.2201397877942716X-RAY DIFFRACTION96.8027210884
2.6679-2.78930.2964966644441430.2220841533772691X-RAY DIFFRACTION96.7896174863
2.7893-2.93630.2938848837091370.2210796560722708X-RAY DIFFRACTION97.1653005464
2.9363-3.12020.2551567115941510.2297965588252716X-RAY DIFFRACTION97.1535072857
3.1202-3.36090.2441710046941460.213884246782708X-RAY DIFFRACTION96.7457627119
3.3609-3.69890.2112536133221110.1923603603012715X-RAY DIFFRACTION96.4834414476
3.6989-4.23340.1806108713311720.1739823613132698X-RAY DIFFRACTION97.1892990179
4.2334-5.3310.1768072196821420.1685461028852733X-RAY DIFFRACTION96.5737319449
5.331-36.38520.2187694156981350.1909011316292753X-RAY DIFFRACTION94.8440065681

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