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- PDB-3vfz: Crystal structure of -35 promoter binding domain of SigD of Mycob... -

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Basic information

Entry
Database: PDB / ID: 3vfz
TitleCrystal structure of -35 promoter binding domain of SigD of Mycobacterium tuberculosis
ComponentsProbable RNA polymerase sigma-D factor
KeywordsTRANSCRIPTION / Transcription regulation / Promoter / Anti-sigma factors
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / response to heat / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like ...RNA polymerase sigma factor 70, region 4 type 2 / Sigma-70, region 4 / RNA polymerase sigma factor 70, ECF, conserved site / Sigma-70 factors ECF subfamily signature. / RNA polymerase sigma-70 like / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ECF RNA polymerase sigma factor SigD / ECF RNA polymerase sigma factor SigD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsJaiswal, R.K. / Thakur, K.G. / Gopal, B.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of sigma-factor activity by proteolysis
Authors: Jaiswal, R.K. / Prabha, T.S. / Manjeera, G. / Gopal, B.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable RNA polymerase sigma-D factor
B: Probable RNA polymerase sigma-D factor


Theoretical massNumber of molelcules
Total (without water)18,9392
Polymers18,9392
Non-polymers00
Water23413
1
A: Probable RNA polymerase sigma-D factor


Theoretical massNumber of molelcules
Total (without water)9,4691
Polymers9,4691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable RNA polymerase sigma-D factor


Theoretical massNumber of molelcules
Total (without water)9,4691
Polymers9,4691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-16 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.430, 35.700, 50.920
Angle α, β, γ (deg.)90.00, 122.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable RNA polymerase sigma-D factor


Mass: 9469.253 Da / Num. of mol.: 2 / Fragment: UNP residues 141-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3414c, sigD / Plasmid: pET Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P66811, UniProt: P9WGG9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.63 Å3/Da / Density % sol: 24.36 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.0-1.3M ammonium sulfate, 0.1M Tris-Cl, 5% 2-Methyl-2,4-pentanediol(MPD), 3% Glycerol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 7, 2010 / Details: Mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→33.883 Å / Num. obs: 9711 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 3.4 / Num. unique all: 10166

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.901→33.883 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.23 / σ(F): 1 / σ(I): 0 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 456 4.81 %RANDOM
Rwork0.1978 ---
obs0.1999 9478 97.05 %-
Solvent computationShrinkage radii: 0.38 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.437 Å2 / ksol: 0.429 e/Å3
Displacement parametersBiso max: 146.15 Å2 / Biso mean: 46.9634 Å2 / Biso min: 19.84 Å2
Baniso -1Baniso -2Baniso -3
1--5.3144 Å2-0 Å2-3.8419 Å2
2--9.6949 Å2-0 Å2
3----4.3805 Å2
Refinement stepCycle: LAST / Resolution: 1.901→33.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 0 13 956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006945
X-RAY DIFFRACTIONf_angle_d0.91277
X-RAY DIFFRACTIONf_chiral_restr0.059167
X-RAY DIFFRACTIONf_plane_restr0.003163
X-RAY DIFFRACTIONf_dihedral_angle_d14.687359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9013-2.17640.27051320.22772865299793
2.1764-2.74180.26851560.18553046320299
2.7418-33.88840.2251680.1973111327999
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)
12.86510.6717-0.42590.5499-0.80023.2360.7349-0.5499-0.57730.4308-0.2264-0.12070.60950.3635-0.22670.5645-0.0338-0.0970.4016-0.0320.4002-20.8652-7.599912.5928
22.8144-0.46170.86050.08620.04013.83250.09920.00340.0371-0.02-0.0874-0.2501-0.6525-0.0652-0.00230.23820.0204-0.02540.21030.02160.3066-16.41683.844114.4438
30.64370.24130.0930.49210.00730.7065-0.03450.12990.03520.3184-0.3207-0.1236-0.10630.1949-0.34960.4243-0.1068-0.06550.28380.14140.2992-12.47039.80138.6393
40.5185-0.0650.07391.4443-0.29080.24290.18570.24810.0773-0.6915-0.15020.04520.14610.08470.02180.30870.04320.00770.4203-0.11280.2015-24.8344-2.60462.5136
51.590.1761-1.13883.0225-1.70743.3911-0.4473-0.05980.1407-0.31550.4143-0.0048-0.0947-1.04780.04650.39990.1338-0.01780.4219-0.03050.3816-26.07228.892513.7158
62.25250.5984-1.63030.76270.44923.86170.51230.458-0.43230.738-0.3563-0.332-2.0036-0.8114-0.02250.69160.1496-0.20850.5971-0.0820.4449-28.07975.631825.9486
72.6990.19850.51020.51220.49650.56070.1035-0.59280.26030.17430.15480.21810.5164-0.5535-0.03490.3357-0.1986-0.04930.43920.12420.3347-25.0273-6.04127.9572
80.6236-0.5296-1.11741.94822.48853.5581-0.1272-0.0432-0.7866-0.3313-0.19780.3995-0.9211-1.13070.08490.25910.083-0.01850.47650.07510.3933-31.88260.991212.6125
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 146:161)A146 - 161
2X-RAY DIFFRACTION2(chain A and resid 162:175)A162 - 175
3X-RAY DIFFRACTION3(chain A and resid 176:195)A176 - 195
4X-RAY DIFFRACTION4(chain A and resid 196:207)A196 - 207
5X-RAY DIFFRACTION5(chain B and resid 146:155)B146 - 155
6X-RAY DIFFRACTION6(chain B and resid 156:163)B156 - 163
7X-RAY DIFFRACTION7(chain B and resid 164:195)B164 - 195
8X-RAY DIFFRACTION8(chain B and resid 196:208)B196 - 208

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