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- PDB-4noi: 2.17 Angstrom Crystal Structure of DNA-directed RNA Polymerase Su... -

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Basic information

Entry
Database: PDB / ID: 4noi
Title2.17 Angstrom Crystal Structure of DNA-directed RNA Polymerase Subunit Alpha from Campylobacter jejuni.
ComponentsDNA-directed RNA polymerase subunit alphaPolymerase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / DNA-directed RNA polymerase subunit alpha
Function / homology
Function and homology information


DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / DNA binding
Similarity search - Function
DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Gyrase A; domain 2 / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / Beta Complex / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type ...DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Gyrase A; domain 2 / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / Beta Complex / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.17 Angstrom Crystal Structure of DNA-directed RNA Polymerase Subunit Alpha from Campylobacter jejuni.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,55419
Polymers81,5982
Non-polymers95617
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-34 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.173, 62.743, 93.621
Angle α, β, γ (deg.)90.00, 112.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-512-

HOH

21B-595-

HOH

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Components

#1: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


Mass: 40799.098 Da / Num. of mol.: 2 / Fragment: DNA-directed RNA polymerase subunit alpha
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Strain: NCTC 11168 / Gene: Cj1595, rpoA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9PM80, DNA-directed RNA polymerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCRYSTAL GREW OVER AN EXTENDED PERIOD AND AUTHORS BELIEVE THAT PEPTIDE HYDROLYZED BETWEEN ILE-237 AND LYS-238.

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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: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 23 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: PACT (F3), 0.2M Sodium iodine, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.17→30 Å / Num. all: 54356 / Num. obs: 54356 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 68.2 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 21.1
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2715 / Rsym value: 0.566 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
SHELXSphasing
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.17→29.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.183 / SU ML: 0.14
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22505 1407 5.1 %RANDOM
Rwork0.17363 ---
all0.1762 26429 --
obs0.1762 26429 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.352 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å2-0.05 Å2
2---1.91 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.17→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3560 0 17 217 3794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023691
X-RAY DIFFRACTIONr_bond_other_d0.0010.023543
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9755013
X-RAY DIFFRACTIONr_angle_other_deg0.70138198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2875457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.20425.509167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16115630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9471510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.024139
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02791
X-RAY DIFFRACTIONr_mcbond_it2.9843.1621816
X-RAY DIFFRACTIONr_mcbond_other2.9773.1621815
X-RAY DIFFRACTIONr_mcangle_it4.1354.7272277
X-RAY DIFFRACTIONr_mcangle_other4.1354.7292278
X-RAY DIFFRACTIONr_scbond_it4.5213.7521875
X-RAY DIFFRACTIONr_scbond_other4.523.7541876
X-RAY DIFFRACTIONr_scangle_other6.775.3912737
X-RAY DIFFRACTIONr_long_range_B_refined8.81426.5854055
X-RAY DIFFRACTIONr_long_range_B_other8.73326.3864008
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 82 -
Rwork0.225 1636 -
obs-1636 84.63 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.3837-0.20841.41130.4495-0.78385.20580.00750.07380.00010.0009-0.0133-0.00910.02620.32210.00580.04280.00220.06410.20680.01390.09811.32495.3551.1078
23.0351.12190.44932.28620.54094.10560.17610.0221-0.0265-0.0815-0.0939-0.2747-0.04390.4133-0.08210.0559-0.03170.04120.0967-0.01180.051812.11588.4983-24.2357
32.5916-0.4271-1.00652.79170.76765.06560.2022-0.00790.2243-0.0284-0.0146-0.1168-0.3270.0034-0.18760.0693-0.04070.06270.0856-0.00620.09177.551614.0732-22.1212
40.44140.64920.46392.0174-0.18191.5487-0.00170.1187-0.0797-0.07990.08240.02930.13980.2447-0.08060.05510.0370.04170.21180.01650.097314.89764.98998.7958
50.59570.32460.23891.3177-0.49241.30420.00780.14070.1107-0.1241-0.06780.0056-0.11090.220.060.05430.00680.01460.11710.04330.094415.187117.96728.1835
62.51210.8725-1.11242.27020.0213.4440.2974-0.23780.27670.3723-0.21420.0167-0.1240.188-0.08320.0747-0.0520.0150.0685-0.02770.072316.400115.322254.9122
72.24651.0907-1.87492.3344-1.74645.7601-0.11910.0677-0.2254-0.2462-0.0361-0.12440.7759-0.07630.15520.1251-0.0223-0.01240.065-0.00040.151113.65234.506343.5822
80.5978-0.064-0.39091.43120.2391.7214-0.04520.21140.1558-0.22360.0387-0.039-0.23980.27170.00650.1352-0.03840.00770.25560.07980.170417.578418.693719.5119
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 72
2X-RAY DIFFRACTION2A73 - 122
3X-RAY DIFFRACTION3A123 - 171
4X-RAY DIFFRACTION4A172 - 230
5X-RAY DIFFRACTION5B9 - 70
6X-RAY DIFFRACTION6B71 - 142
7X-RAY DIFFRACTION7B143 - 177
8X-RAY DIFFRACTION8B178 - 231

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