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- PDB-3vep: Crystal structure of SigD4 in complex with its negative regulator RsdA -

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Basic information

Entry
Database: PDB / ID: 3vep
TitleCrystal structure of SigD4 in complex with its negative regulator RsdA
Components
  • Probable RNA polymerase sigma-D factor
  • Uncharacterized protein Rv3413c/MT3522
KeywordsMEMBRANE PROTEIN/TRANSCRIPTION / Sigma factor / promoter DNA / anti-sigma factor / MEMBRANE PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / response to heat / membrane => GO:0016020 / regulation of DNA-templated transcription / DNA binding / extracellular region / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1300 / Anti-sigma-D factor RsdA, sigma factor binding region / Anti-sigma-D factor RsdA to sigma factor binding region / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1300 / Anti-sigma-D factor RsdA, sigma factor binding region / Anti-sigma-D factor RsdA to sigma factor binding region / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Anti-sigma-D factor RsdA / ECF RNA polymerase sigma factor SigD / ECF RNA polymerase sigma factor SigD / Anti-sigma-D factor RsdA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJaiswal, R.K. / 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 9, 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

Downloads & links

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Assembly

Deposited unit
X: Uncharacterized protein Rv3413c/MT3522
D: Probable RNA polymerase sigma-D factor
C: Uncharacterized protein Rv3413c/MT3522
A: Probable RNA polymerase sigma-D factor
G: Uncharacterized protein Rv3413c/MT3522
E: Probable RNA polymerase sigma-D factor
J: Uncharacterized protein Rv3413c/MT3522
H: Probable RNA polymerase sigma-D factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,81721
Polymers73,5688
Non-polymers1,24913
Water93752
1
X: Uncharacterized protein Rv3413c/MT3522
D: Probable RNA polymerase sigma-D factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6805
Polymers18,3922
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-67 kcal/mol
Surface area7210 Å2
MethodPISA
2
C: Uncharacterized protein Rv3413c/MT3522
A: Probable RNA polymerase sigma-D factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6805
Polymers18,3922
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-38 kcal/mol
Surface area7330 Å2
MethodPISA
3
G: Uncharacterized protein Rv3413c/MT3522
E: Probable RNA polymerase sigma-D factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6805
Polymers18,3922
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-65 kcal/mol
Surface area7390 Å2
MethodPISA
4
J: Uncharacterized protein Rv3413c/MT3522
H: Probable RNA polymerase sigma-D factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7766
Polymers18,3922
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-52 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.740, 110.720, 73.130
Angle α, β, γ (deg.)90.00, 133.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
31E
41H
12X
22C
32G
42J

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain D and (resseq 1:68 )D1 - 68
211chain A and (resseq 1:70 )A1 - 70
311chain E and (resseq 1:70 )E1 - 70
411chain H and (resseq 1:71 )H1 - 71
112chain X and (resseq 12:57 )X12 - 57
212chain C and (resseq 12:58 )C12 - 58
312chain G and (resseq 11:57 )G11 - 57
412chain J and (resseq 12:58 )J12 - 58

NCS ensembles :
ID
1
2

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Components

#1: Protein
Uncharacterized protein Rv3413c/MT3522


Mass: 8922.765 Da / Num. of mol.: 4 / Fragment: UNP residues 1-80
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv3413c / Plasmid: pET Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P65081, UniProt: P9WJ71*PLUS
#2: Protein
Probable RNA polymerase sigma-D factor


Mass: 9469.253 Da / Num. of mol.: 4 / Fragment: UNP residues 141-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: sigD, Rv3414c / Plasmid: pET Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P66811, UniProt: P9WGG9*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 300 K / Method: oil-batch / pH: 7.4
Details: 1.0-103M Ammonium Sulphate, 0.1M HEPES, 15-20% PEG 4000, pH 7.4, OIL-BATCH, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 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: 2.5→38.465 Å / Num. obs: 18114 / % possible obs: 86.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 4.4 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→38.465 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7536 / SU ML: 0.43 / σ(F): 2 / σ(I): 4 / Phase error: 31.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2866 902 5.17 %RANDOM
Rwork0.2427 ---
obs0.245 17437 86.6 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.232 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso max: 128.79 Å2 / Biso mean: 53.6172 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-9.0236 Å2-0 Å2-1.4024 Å2
2---12.816 Å20 Å2
3---3.7924 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 65 52 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123676
X-RAY DIFFRACTIONf_angle_d1.6065009
X-RAY DIFFRACTIONf_chiral_restr0.135598
X-RAY DIFFRACTIONf_plane_restr0.012652
X-RAY DIFFRACTIONf_dihedral_angle_d19.7921352
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11D485X-RAY DIFFRACTIONPOSITIONAL0.088
12A485X-RAY DIFFRACTIONPOSITIONAL0.088
13E503X-RAY DIFFRACTIONPOSITIONAL0.066
14H498X-RAY DIFFRACTIONPOSITIONAL0.084
21X371X-RAY DIFFRACTIONPOSITIONAL0.084
22C371X-RAY DIFFRACTIONPOSITIONAL0.084
23G372X-RAY DIFFRACTIONPOSITIONAL0.054
24J364X-RAY DIFFRACTIONPOSITIONAL0.065
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5003-2.65690.36131340.28632688282288
2.6569-2.86190.3371430.27522416255993
2.8619-3.14980.34491640.25423078324297
3.1498-3.60530.26931460.24772730287686
3.6053-4.54120.27941410.21512451259277
4.5412-38.46950.25761740.24163172334699

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