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- PDB-4iqz: The crystal structure of a large insert in RNA polymerase (RpoC) ... -

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Basic information

Entry
Database: PDB / ID: 4iqz
TitleThe crystal structure of a large insert in RNA polymerase (RpoC) subunit from E. coli
ComponentsDNA-directed RNA polymerase subunit beta'Polymerase
KeywordsUNKNOWN FUNCTION / Function of insertion is unknown
Function / homology
Function and homology information


submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination ...submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / DNA-templated transcription initiation / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit ...RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBhandari, V. / Sugiman-Marangos, S.N. / Naushad, H.S. / Gupta, R.S. / Junop, M.S.
CitationJournal: To be Published
Title: The crystal structure of a large insert in RNA polymerase (RpoC) subunit from E. coli
Authors: Bhandari, V. / Sugiman-Marangos, S.N. / Naushad, H.S. / Gupta, R.S. / Junop, M.S.
History
DepositionJan 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release

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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 beta'
B: DNA-directed RNA polymerase subunit beta'
C: DNA-directed RNA polymerase subunit beta'
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit beta'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,93868
Polymers133,6715
Non-polymers7,26863
Water9,512528
1
A: DNA-directed RNA polymerase subunit beta'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,68418
Polymers26,7341
Non-polymers1,95017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-directed RNA polymerase subunit beta'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,40715
Polymers26,7341
Non-polymers1,67314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA-directed RNA polymerase subunit beta'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,17614
Polymers26,7341
Non-polymers1,44213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA-directed RNA polymerase subunit beta'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,40715
Polymers26,7341
Non-polymers1,67314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: DNA-directed RNA polymerase subunit beta'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2656
Polymers26,7341
Non-polymers5315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)198.060, 65.630, 81.292
Angle α, β, γ (deg.)90.00, 108.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

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Components

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


Mass: 26734.111 Da / Num. of mol.: 5 / Fragment: unp residues 932-1141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 MG1655 / Gene: b3988, JW3951, rpoC, RPOC subunit beta', tabB / Plasmid: pET-15b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P0A8T7, DNA-directed RNA polymerase
#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 1.87 Å3/Da / Density % sol: 34.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.2 M KCl, 0.04 M Tris pH 7.9, 0.1 M Phosphate-Citrate, 1.6 M Sodium di-Hydrogen Phosphate, 0.4 M di-Potassium Hydrogen Phosphate, 0.05 M Sodium Iodide , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9802 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2010
RadiationMonochromator: Si (iii) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9802 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 58175 / Num. obs: 58175 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 29.03 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 13.85
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.79 / Num. unique all: 2880 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→35.987 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 2947 5.07 %Random
Rwork0.2034 ---
obs0.2053 58074 97.84 %-
all-58175 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5872 0 63 528 6463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095937
X-RAY DIFFRACTIONf_angle_d1.1988103
X-RAY DIFFRACTIONf_dihedral_angle_d12.1832002
X-RAY DIFFRACTIONf_chiral_restr0.071033
X-RAY DIFFRACTIONf_plane_restr0.0041043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0819-2.11610.26891270.2262237X-RAY DIFFRACTION85
2.1161-2.15260.28351480.21392569X-RAY DIFFRACTION98
2.1526-2.19170.29121310.21762637X-RAY DIFFRACTION98
2.1917-2.23380.28331380.21582603X-RAY DIFFRACTION98
2.2338-2.27940.25811290.20872650X-RAY DIFFRACTION98
2.2794-2.3290.23181130.20882676X-RAY DIFFRACTION98
2.329-2.38320.27081370.21622587X-RAY DIFFRACTION99
2.3832-2.44270.29761330.22562678X-RAY DIFFRACTION99
2.4427-2.50880.29271280.22262632X-RAY DIFFRACTION99
2.5088-2.58260.27411570.22832634X-RAY DIFFRACTION99
2.5826-2.66590.30121150.21962667X-RAY DIFFRACTION99
2.6659-2.76120.25841430.21542663X-RAY DIFFRACTION99
2.7612-2.87170.24061610.21232617X-RAY DIFFRACTION99
2.8717-3.00230.23491420.22022695X-RAY DIFFRACTION99
3.0023-3.16050.2711540.21122667X-RAY DIFFRACTION99
3.1605-3.35840.24051560.20052627X-RAY DIFFRACTION99
3.3584-3.61750.19881570.17572621X-RAY DIFFRACTION98
3.6175-3.98110.21821540.17842624X-RAY DIFFRACTION98
3.9811-4.55620.20671450.16172688X-RAY DIFFRACTION99
4.5562-5.73650.21691470.19572676X-RAY DIFFRACTION99
5.7365-35.99240.24021320.2482679X-RAY DIFFRACTION95
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)
14.6331-0.55431.0081.0079-0.46852.15840.01820.1735-0.14480.0073-0.012-0.0860.04970.2160.00170.12960.01210.0280.14790.00150.138780.301524.705529.7163
27.42563.47167.39642.08843.66758.07250.2859-0.96410.24490.4058-0.2374-0.13220.1671-0.6585-0.04970.15470.02280.00860.1840.00020.232867.761131.74536.5444
33.6457-0.7844-3.16673.06711.84445.3489-0.4885-0.36590.04360.61210.07750.37630.3283-0.42010.23460.17410.0610.02510.2717-0.04140.235650.323131.298928.8082
47.612-0.4631-2.06334.8467-0.5966.9638-0.0464-0.71960.39040.3632-0.4160.0751-0.2705-0.43070.29510.26260.03630.02890.3387-0.12410.306548.377135.781640.5454
52.87520.90380.61232.10080.20654.5669-0.0698-0.0514-0.30390.05430.07350.05370.672-0.32520.00860.19040.0151-0.00560.13410.03070.268552.298523.675126.6837
60.4919-0.6222-1.34643.01-0.1565.4044-0.1129-0.1279-0.04040.19850.11060.1959-0.50240.49060.03950.1396-0.03390.02550.11950.02270.152458.964634.0729.3167
71.2432-0.4345-0.01571.0108-0.62960.76980.0355-0.3438-0.8453-0.08640.10210.30120.6757-0.58550.02170.3681-0.17790.02080.44920.10490.463143.605613.632436.6683
83.3324-0.41261.98313.0421-2.10237.67840.08790.28390.1101-0.19460.03940.26720.0276-0.2201-0.12540.2235-0.0638-0.00050.20520.11420.286845.819315.144132.7429
95.46555.32656.33615.18786.14418.30980.282-0.1167-0.55470.2861-0.03150.33831.2983-0.0228-0.34220.35250.0259-0.04720.18990.020.381856.3038.482142.3901
103.5988-1.6070.20064.7277-0.33985.5820.1105-0.5554-0.59530.21890.1098-0.15360.64450.6087-0.16680.3238-0.0397-0.01190.34950.07470.37770.525511.330952.8495
113.7178-0.2349-0.37723.8142-0.20473.86520.1138-0.41040.04940.2625-0.03690.32330.02950.0612-0.0630.2016-0.09350.0510.24660.03470.211562.200418.017753.5916
123.5101-2.36080.38785.3-0.57313.88540.0371-0.0518-0.2299-0.1728-0.1281-0.3960.27030.02170.10160.2317-0.0333-0.01220.1440.0740.27774.769947.4229-7.3456
132.5606-1.52940.09781.12190.03660.06470.0520.3836-0.1984-0.62240.1392-0.5631-0.00450.2701-0.10440.3304-0.00170.13610.1932-0.05380.276476.598635.8466-16.1625
140.6288-1.8829-0.94928.65356.02348.33230.0844-0.0434-0.3181-0.17350.1489-0.241-0.04310.2661-0.2290.1740.0141-0.00350.24630.05680.295177.074443.6739-7.1761
155.1008-2.7006-6.24263.52262.78977.93460.39180.32780.2958-1.10560.4117-0.8781-0.7525-0.084-0.73110.3711-0.01780.12490.18340.0560.355181.771347.2609-13.973
163.4434-1.1863-1.67292.1755-0.55523.1220.1866-0.4002-0.06150.3838-0.0482-0.1267-0.19470.2036-0.11050.4173-0.1085-0.02940.1720.03860.337671.111757.64074.9189
176.54271.9993-2.54623.8038-3.35153.07840.7987-0.0565-0.33130.98710.2591-0.2746-0.28570.1048-0.70920.9295-0.2294-0.01410.7731-0.2580.608370.587967.566419.425
183.00251.773-4.90816.1161-3.60349.10510.967-0.67310.38520.8776-0.7241-0.2399-0.06621.9133-0.32940.6055-0.2375-0.09780.58730.00150.45178.713166.020615.9428
198.73660.57865.15072.64081.21056.48040.5362-1.0830.9420.7289-0.0595-0.3341-0.5537-1.0448-0.17840.5886-0.03630.10970.2942-0.03960.468162.341563.743613.8501
204.4392-0.17394.05763.6898-1.66864.3613-0.08750.0087-1.86640.76820.32890.88691.5352-1.597-0.16120.4802-0.13140.14760.35840.04860.655354.507455.19085.2872
215.12154.0420.05944.32411.25442.31230.384-0.08580.1230.11910.0250.30020.0438-0.141-0.33630.2711-0.0240.02490.13790.09870.297367.601758.048812.7305
222.18411.19511.0681.08840.2262.43560.24720.19050.0947-0.1015-0.2167-0.1459-0.35110.23860.07240.4254-0.08710.02360.18060.0360.264571.739562.495.0365
231.0533-1.6631-1.19932.90031.70871.4779-0.24630.07320.48220.2834-0.41741.0184-0.0638-0.16110.66070.3634-0.052-0.09280.19550.00550.67551.962651.361119.5222
246.2227-0.4932-1.99354.5961-0.50124.94350.1243-0.37720.23780.28-0.01810.6888-0.58140.0638-0.06570.36140.00340.01680.11810.01650.312759.294748.701220.1278
254.70852.6151-0.33513.6189-0.39136.05260.0576-0.2046-0.00240.3-0.22810.8197-0.5516-0.30230.16150.1925-0.026-0.01470.1414-0.04440.274756.475152.22817.1983
262.30481.58140.51553.85671.31832.7595-0.1061-0.0731-0.16610.12480.0990.3157-0.2241-0.2219-0.00210.2682-0.0235-0.02070.24240.09990.249461.878941.934214.7556
270.4687-1.3824-0.48096.32762.37022.0618-0.14620.1113-0.133-0.26460.17230.06320.08740.498-0.02470.1831-0.03990.01590.3210.04220.246579.330431.34349.1253
288.095-2.7502-0.33693.4791-3.16395.11550.00851.3165-0.3683-0.62140.50580.58640.74140.4531-0.55250.319-0.0944-0.0550.3389-0.02990.278369.335429.53861.7367
295.01772.59511.0326.98531.33314.2545-0.1004-0.0585-0.17210.1738-0.2007-0.54830.4041.02040.00890.19430.00430.00630.2930.08730.182680.425333.238514.6257
305.79131.85690.03962.8239-1.57165.2979-0.3495-0.9073-0.62931.3183-0.3192-0.4612-0.19280.39880.47080.42960.0344-0.08270.45550.01830.304180.205939.771225.8386
313.6603-1.46673.25864.10371.61645.88450.0497-0.3085-0.24680.08830.1197-0.2457-0.24030.0103-0.17570.2034-0.07160.01110.26150.04010.156672.302431.766615.8862
320.2466-0.15410.12231.55330.09542.2533-0.3220.20350.3447-0.27150.23470.2071-0.2410.38810.10480.23-0.0616-0.05610.22390.07770.247174.005541.9679.1062
337.01562.79941.92196.56621.69345.80550.11120.2335-0.18470.045-0.23370.0262-0.2005-0.52260.10880.1602-0.036-0.00920.22660.04330.160263.835135.397911.6756
344.8414-1.0302-2.51213.12441.26386.78860.09570.85690.092-0.7076-0.0983-0.37990.0833-0.48550.00430.32940.0650.06690.4318-0.09640.325816.08446.02528.741
351.4309-0.80381.63576.7274-3.32185.43840.11170.2720.2319-0.2944-0.0896-0.1622-0.1637-0.3654-0.01220.31340.06840.10540.3593-0.02620.320918.788948.84636.5621
364.0365-0.3232-0.49340.872-0.371.2044-0.4794-0.4350.49020.48780.2127-0.0499-0.261-0.06890.26230.37310.0901-0.06050.2869-0.0210.382332.685128.39823.251
373.76380.331-0.78833.9004-0.2643.2267-0.08320.0145-0.13360.54180.0551-0.1159-0.1563-0.09820.04670.27250.0774-0.03340.1761-0.06540.201327.844426.815417.1563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 34 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 117 )
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 134 )
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 165 )
5X-RAY DIFFRACTION5chain 'A' and (resid 166 through 194 )
6X-RAY DIFFRACTION6chain 'A' and (resid 195 through 216 )
7X-RAY DIFFRACTION7chain 'B' and (resid 37 through 86 )
8X-RAY DIFFRACTION8chain 'B' and (resid 87 through 108 )
9X-RAY DIFFRACTION9chain 'B' and (resid 109 through 117 )
10X-RAY DIFFRACTION10chain 'B' and (resid 118 through 159 )
11X-RAY DIFFRACTION11chain 'B' and (resid 160 through 216 )
12X-RAY DIFFRACTION12chain 'C' and (resid 36 through 68 )
13X-RAY DIFFRACTION13chain 'C' and (resid 69 through 79 )
14X-RAY DIFFRACTION14chain 'C' and (resid 80 through 96 )
15X-RAY DIFFRACTION15chain 'C' and (resid 97 through 108 )
16X-RAY DIFFRACTION16chain 'C' and (resid 109 through 127 )
17X-RAY DIFFRACTION17chain 'C' and (resid 128 through 137 )
18X-RAY DIFFRACTION18chain 'C' and (resid 138 through 155 )
19X-RAY DIFFRACTION19chain 'C' and (resid 156 through 175 )
20X-RAY DIFFRACTION20chain 'C' and (resid 176 through 185 )
21X-RAY DIFFRACTION21chain 'C' and (resid 186 through 194 )
22X-RAY DIFFRACTION22chain 'C' and (resid 195 through 215 )
23X-RAY DIFFRACTION23chain 'D' and (resid 37 through 53 )
24X-RAY DIFFRACTION24chain 'D' and (resid 54 through 86 )
25X-RAY DIFFRACTION25chain 'D' and (resid 87 through 104 )
26X-RAY DIFFRACTION26chain 'D' and (resid 105 through 122 )
27X-RAY DIFFRACTION27chain 'D' and (resid 123 through 134 )
28X-RAY DIFFRACTION28chain 'D' and (resid 135 through 150 )
29X-RAY DIFFRACTION29chain 'D' and (resid 151 through 175 )
30X-RAY DIFFRACTION30chain 'D' and (resid 176 through 185 )
31X-RAY DIFFRACTION31chain 'D' and (resid 186 through 194 )
32X-RAY DIFFRACTION32chain 'D' and (resid 195 through 208 )
33X-RAY DIFFRACTION33chain 'D' and (resid 209 through 215 )
34X-RAY DIFFRACTION34chain 'E' and (resid 37 through 68 )
35X-RAY DIFFRACTION35chain 'E' and (resid 69 through 117 )
36X-RAY DIFFRACTION36chain 'E' and (resid 118 through 145 )
37X-RAY DIFFRACTION37chain 'E' and (resid 146 through 216 )

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