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- PDB-4v8s: Archaeal RNAP-DNA binary complex at 4.32Ang -

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Basic information

Entry
Database: PDB / ID: 4v8s
TitleArchaeal RNAP-DNA binary complex at 4.32Ang
Components
  • (DNA-DIRECTED RNA ...) x 9
  • (RNA POLYMERASE SUBUNIT ...) x 4
  • 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'
  • 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'
KeywordsTRANSFERASE/DNA / TRANSFERASE-DNA COMPLEX / TRANSCRIPTION
Function / homology
Function and homology information


RNA polymerase complex / 3 iron, 4 sulfur cluster binding / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 4 iron, 4 sulfur cluster binding / transcription, DNA-templated / protein dimerization activity / nucleotide binding ...RNA polymerase complex / 3 iron, 4 sulfur cluster binding / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / 4 iron, 4 sulfur cluster binding / transcription, DNA-templated / protein dimerization activity / nucleotide binding / DNA binding / zinc ion binding / metal ion binding
Similarity search - Function
RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo3 ...RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase, subunit E/RPC8 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases N / 8 kDa subunit / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit RPB10 / RNA polymerase subunit CX / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase, subunit H/Rpb5 C-terminal / RPB5-like RNA polymerase subunit superfamily / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / : / : / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerase Rpb5, C-terminal domain / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA-binding domain, S1 / S1 RNA binding domain / Ribosomal protein S1-like RNA-binding domain / S1 domain / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb2, domain 2 superfamily / : / RNA polymerase, N-terminal / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb3/RpoA insert domain / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb2, domain 7 / RNA polymerase, beta subunit, conserved site / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo8 / IRON/SULFUR CLUSTER / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo3 ...DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo8 / IRON/SULFUR CLUSTER / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA (> 10) / DNA / DNA-directed RNA polymerase subunit Rpo13
Similarity search - Component
Biological speciesSULFOLOBUS SHIBATAE B12 (archaea)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.323 Å
AuthorsWojtas, M.N. / Mogni, M. / Millet, O. / Bell, S.D. / Abrescia, N.G.A.
Citation
Journal: Nucleic Acids Res. / Year: 2012
Title: Structural and Functional Analyses of the Interaction of Archaeal RNA Polymerase with DNA.
Authors: Wojtas, M.N. / Mogni, M. / Millet, O. / Bell, S.D. / Abrescia, N.G.A.
#1: Journal: Biochem.Soc.Trans. / Year: 2011
Title: Archaeal RNA Polymerase: The Influence of the Protruding Stalk in Crystal Packing and Preliminary Biophysical Analysis of the Rpo13 Subunit.
Authors: Wojtas, M. / Peralta, B. / Ondiviela, M. / Mogni, M. / Bell, S.D. / Abrescia, N.G.A.
#2: Journal: Plos Biol. / Year: 2009
Title: Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure.
Authors: Korkhin, Y. / Unligil, U.M. / Littlefield, O. / Nelson, P.J. / Stuart, D.I. / Sigler, P.B. / Bell, S.D. / Abrescia, N.G.A.
History
DepositionJul 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4B1O, 4B1P
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "RQ" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "RQ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "TB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AC: 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'
AD: 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'
AI: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
AJ: RNA POLYMERASE SUBUNIT 13
AM: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
AO: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
AR: DNA-DIRECTED RNA POLYMERASE
AS: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
AT: RNA POLYMERASE SUBUNIT 7
AU: RNA POLYMERASE SUBUNIT 4
AV: RNA POLYMERASE SUBUNIT 8
AW: DNA-DIRECTED RNA POLYMERASE
AX: DNA-DIRECTED RNA POLYMERASE SUBUNIT P
AY: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
AZ: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
BA: DNA-DIRECTED RNA POLYMERASE
BB: DNA-DIRECTED RNA POLYMERASE
BC: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
BD: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
BE: RNA POLYMERASE SUBUNIT 7
BF: RNA POLYMERASE SUBUNIT 4
BG: RNA POLYMERASE SUBUNIT 8
BH: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
BK: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
BL: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
BN: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
BP: DNA-DIRECTED RNA POLYMERASE SUBUNIT P
BQ: RNA POLYMERASE SUBUNIT 13
BR: 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'
BS: 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)831,15846
Polymers829,62130
Non-polymers1,53716
Water0
1
AC: 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'
AD: 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'
AI: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
AJ: RNA POLYMERASE SUBUNIT 13
AM: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
AO: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
AR: DNA-DIRECTED RNA POLYMERASE
AS: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
AT: RNA POLYMERASE SUBUNIT 7
AU: RNA POLYMERASE SUBUNIT 4
AV: RNA POLYMERASE SUBUNIT 8
AW: DNA-DIRECTED RNA POLYMERASE
AX: DNA-DIRECTED RNA POLYMERASE SUBUNIT P
AY: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
AZ: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,57923
Polymers414,81115
Non-polymers7688
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BA: DNA-DIRECTED RNA POLYMERASE
BB: DNA-DIRECTED RNA POLYMERASE
BC: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
BD: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
BE: RNA POLYMERASE SUBUNIT 7
BF: RNA POLYMERASE SUBUNIT 4
BG: RNA POLYMERASE SUBUNIT 8
BH: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
BK: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
BL: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
BN: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
BP: DNA-DIRECTED RNA POLYMERASE SUBUNIT P
BQ: RNA POLYMERASE SUBUNIT 13
BR: 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'
BS: 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,57923
Polymers414,81115
Non-polymers7688
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)134.134, 199.416, 214.246
Angle α, β, γ (deg.)90.00, 103.54, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28
19
29
110
210
111
211
112
212
113
213
114
214
115
215

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN BB AND (RESSEQ 7:510 OR RESSEQ 516:821 OR RESSEQ...
211CHAIN AR AND (RESSEQ 7:510 OR RESSEQ 516:821 OR RESSEQ...
112CHAIN AA AND (RESSEQ 3:222 OR RESSEQ 228:879 OR RESSEQ...
212CHAIN BW AND (RESSEQ 3:222 OR RESSEQ 228:879 OR RESSEQ...
113CHAIN BC AND (RESSEQ 6:86 OR RESSEQ 100:394 ) AND (NOT ELEMENT H)
213CHAIN AY AND (RESSEQ 6:86 OR RESSEQ 100:394 ) AND (NOT ELEMENT H)
114CHAIN BD AND (RESSEQ 2:263 OR RESSEQ 1001:1001 ) AND (NOT ELEMENT H)
214CHAIN AS AND (RESSEQ 2:263 OR RESSEQ 1001:1001 ) AND (NOT ELEMENT H)
115CHAIN BE AND (RESSEQ 1:151 OR RESSEQ 159:178 ) AND (NOT ELEMENT H)
215CHAIN AT AND (RESSEQ 1:151 OR RESSEQ 159:178 ) AND (NOT ELEMENT H)
116CHAIN BG AND (RESSEQ 5:117 ) AND (NOT ELEMENT H)
216CHAIN AV AND (RESSEQ 5:117 ) AND (NOT ELEMENT H)
117CHAIN BL AND (RESSEQ 1:91 ) AND (NOT ELEMENT H)
217CHAIN AM AND (RESSEQ 1:91 ) AND (NOT ELEMENT H)
118CHAIN BF AND (RESSEQ 3:107 ) AND (NOT ELEMENT H)
218CHAIN AU AND (RESSEQ 3:107 ) AND (NOT ELEMENT H)
119CHAIN BK AND (RESSEQ 11:94 ) AND (NOT ELEMENT H)
219CHAIN AI AND (RESSEQ 11:94 ) AND (NOT ELEMENT H)
1110CHAIN BH AND (RESSEQ 8:83 ) AND (NOT ELEMENT H)
2110CHAIN AZ AND (RESSEQ 8:83 ) AND (NOT ELEMENT H)
1111CHAIN BN AND (RESSEQ 1:65 OR RESSEQ 100:100 ) AND (NOT ELEMENT H)
2111CHAIN AO AND (RESSEQ 1:65 OR RESSEQ 100:100 ) AND (NOT ELEMENT H)
1112CHAIN BQ AND (RESSEQ 32:81 ) AND (NOT ELEMENT H)
2112CHAIN AJ AND (RESSEQ 33:81 ) AND (NOT ELEMENT H)
1113CHAIN BP AND (RESSEQ 5:48 OR RESSEQ 50:50 ) AND (NOT ELEMENT H)
2113CHAIN AX AND (RESSEQ 5:48 OR RESSEQ 50:50 ) AND (NOT ELEMENT H)
1114CHAIN BR AND (RESSEQ 1:14 ) AND (NOT ELEMENT H)
2114CHAIN AC AND (RESSEQ 1:13 ) AND (NOT ELEMENT H)
1115CHAIN BS AND (RESSEQ 2:17 ) AND (NOT ELEMENT H)
2115CHAIN AD AND (RESSEQ 3:17 ) AND (NOT ELEMENT H)

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(0.885368, -0.000197, 0.46489), (-0.000404, -1, 0.000346), (0.46489, -0.000495, -0.885368)-17.5242, 0.97464, 73.0054
2given(0.884904, 0.000322, 0.465773), (-0.000458, -0.999999, 0.001562), (0.465773, -0.001595, -0.884903)-17.8278, 0.92819, 72.877
3given(0.888171, -0.000465, 0.459512), (8.0E-5, -0.999999, -0.001167), (0.459513, 0.001074, -0.888171)-17.7753, 0.87557, 72.9867
4given(0.885738, 0.008986, 0.464099), (0.007421, -0.999959, 0.005199), (0.464126, -0.001161, -0.885768)-18.4488, 0.15513, 73.5251
5given(0.886208, 0.007163, 0.463232), (9.6E-5, -0.999883, 0.015278), (0.463288, -0.013495, -0.886105)-18.6175, 0.0334, 73.7934
6given(0.890748, -0.011391, 0.454355), (-0.011904, -0.999928, -0.001733), (0.454342, -0.003865, -0.890819)-17.8369, 2.09797, 74.3844
7given(0.886512, -0.00033, 0.462705), (-0.001808, -0.999995, 0.002751), (0.462701, -0.003275, -0.886508)-18.1802, 0.99672, 73.6236
8given(0.874996, -0.002785, 0.484122), (0.018672, -0.999045, -0.039497), (0.48377, 0.043599, -0.874109)-18.6897, 3.15934, 67.7999
9given(0.884357, -0.001604, 0.466809), (-0.000526, -0.999997, -0.002439), (0.466811, 0.001912, -0.884355)-18.1468, 1.06673, 72.4899
10given(0.886773, 0.010436, 0.462087), (0.010984, -0.999939, 0.001504), (0.462074, 0.003742, -0.886834)-18.163, 0.47149, 72.6002
11given(0.885157, 0.005504, 0.46526), (-0.001872, -0.99988, 0.015391), (0.465288, -0.014494, -0.88504)-18.0104, 0.86423, 74.1794
12given(0.890021, -0.016838, 0.455609), (-0.031801, -0.999177, 0.025196), (0.454809, -0.036914, -0.889823)-17.372, 0.091, 74.3282
13given(0.88678, -0.001316, 0.462189), (-0.005319, -0.999959, 0.007359), (0.46216, -0.008984, -0.886751)-17.4611, 1.28646, 74.0631
14given(0.924118, -0.062296, 0.376995), (0.021083, -0.976805, -0.21309), (0.381525, 0.204869, -0.90137)-17.0414, 2.59576, 69.2878
15given(0.924327, -0.059168, 0.376987), (0.02366, -0.97712, -0.21137), (0.380867, 0.204295, -0.901778)-17.1388, 2.51038, 69.2964

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Components

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DNA chain , 2 types, 4 molecules ACBRADBS

#1: DNA chain 5'-D(*TP*CP*TP*TP*AP*TP*AP*CP*TP*CP*TP*AP*TP*CP)-3'


Mass: 4180.739 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: DNA chain 5'-D(*AP*TP*AP*GP*AP*GP*TP*AP*TP*AP*AP*GP*AP*TP *AP*G)-3'


Mass: 4994.292 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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DNA-DIRECTED RNA ... , 9 types, 18 molecules AIBKAMBLAOBNARBBASBDAWBAAXBPAYBCAZBH

#3: Protein DNA-DIRECTED RNA POLYMERASE SUBUNIT K / Polymerase


Mass: 10729.534 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO6 / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB61, DNA-directed RNA polymerase
#5: Protein DNA-DIRECTED RNA POLYMERASE SUBUNIT L / Polymerase


Mass: 10211.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO11 / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB62, DNA-directed RNA polymerase
#6: Protein DNA-DIRECTED RNA POLYMERASE SUBUNIT N / Polymerase


Mass: 7617.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO10 / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB63, DNA-directed RNA polymerase
#7: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 127582.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO2 / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB55, DNA-directed RNA polymerase
#8: Protein DNA-DIRECTED RNA POLYMERASE SUBUNIT D / Polymerase


Mass: 30179.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO3 / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB56, DNA-directed RNA polymerase
#12: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 99766.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO1N SUBUNIT / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB53, DNA-directed RNA polymerase
#13: Protein/peptide DNA-DIRECTED RNA POLYMERASE SUBUNIT P / Polymerase


Mass: 5606.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO12 / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB64, DNA-directed RNA polymerase
#14: Protein DNA-DIRECTED RNA POLYMERASE SUBUNIT A'' / Polymerase


Mass: 43792.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO1C / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB54, DNA-directed RNA polymerase
#15: Protein DNA-DIRECTED RNA POLYMERASE SUBUNIT H / Polymerase


Mass: 9688.296 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO5 / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB60, DNA-directed RNA polymerase

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RNA POLYMERASE SUBUNIT ... , 4 types, 8 molecules AJBQATBEAUBFAVBG

#4: Protein RNA POLYMERASE SUBUNIT 13 /


Mass: 12170.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB65
#9: Protein RNA POLYMERASE SUBUNIT 7 /


Mass: 20328.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO7 / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB57
#10: Protein RNA POLYMERASE SUBUNIT 4 /


Mass: 12822.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPOF / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB58
#11: Protein RNA POLYMERASE SUBUNIT 8 /


Mass: 15139.458 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO8 / Source: (natural) SULFOLOBUS SHIBATAE B12 (archaea) / References: UniProt: B8YB59

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Non-polymers , 3 types, 16 molecules

#16: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#17: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 3.76 Å3/Da / Density % sol: 67.27 % / Description: NONE
Crystal growpH: 6.5
Details: PLEASE SEE PRIMARY REFERENCE AND WOJTAS MN & ABRESCIA NGA, SUBMITTED, pH 6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.033
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: BENT COLLIMATING MIRROR AND TOROID
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 4.3→60 Å / Num. obs: 65048 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 105.24 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 6
Reflection shellResolution: 4.3→4.45 Å / Redundancy: 4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2 / % possible all: 77.8

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Processing

Software
NameVersionClassification
PHASERmodel building
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AYB
Resolution: 4.323→50.424 Å / SU ML: 0.58 / σ(F): 1.34 / Phase error: 33.37 / Stereochemistry target values: ML
Details: AS IN THE APO-RNAP STRUCTURE PDB 4AYB WE CAN SEE ADDITIONAL DENSITY BETWEEN ASP 178 AND GLU 444 IN CHAIN B -AND R- POSSIBLY ATTRIBUTABLE TO A DIVALENT ION
RfactorNum. reflection% reflection
Rfree0.3105 3301 5.1 %
Rwork0.2917 --
obs0.2926 64957 88.56 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 114.371 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 173.91 Å2
Baniso -1Baniso -2Baniso -3
1-62.6028 Å20 Å254.0591 Å2
2---26.0386 Å20 Å2
3----36.5642 Å2
Refinement stepCycle: LAST / Resolution: 4.323→50.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27092 575 14 0 27681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00556636
X-RAY DIFFRACTIONf_angle_d0.66776685
X-RAY DIFFRACTIONf_dihedral_angle_d12.91321764
X-RAY DIFFRACTIONf_chiral_restr0.048717
X-RAY DIFFRACTIONf_plane_restr0.0039618
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11BB8757X-RAY DIFFRACTIONPOSITIONAL
12AR8757X-RAY DIFFRACTIONPOSITIONAL0.007
21BA6961X-RAY DIFFRACTIONPOSITIONAL
22AW6961X-RAY DIFFRACTIONPOSITIONAL0.011
31BC2906X-RAY DIFFRACTIONPOSITIONAL
32AY2906X-RAY DIFFRACTIONPOSITIONAL0.006
41BD2094X-RAY DIFFRACTIONPOSITIONAL
42AS2094X-RAY DIFFRACTIONPOSITIONAL0.01
51BE1359X-RAY DIFFRACTIONPOSITIONAL
52AT1359X-RAY DIFFRACTIONPOSITIONAL0.005
61BG901X-RAY DIFFRACTIONPOSITIONAL
62AV901X-RAY DIFFRACTIONPOSITIONAL0.008
71BL707X-RAY DIFFRACTIONPOSITIONAL
72AM707X-RAY DIFFRACTIONPOSITIONAL0.01
81BF827X-RAY DIFFRACTIONPOSITIONAL
82AU827X-RAY DIFFRACTIONPOSITIONAL0.007
91BK673X-RAY DIFFRACTIONPOSITIONAL
92AI673X-RAY DIFFRACTIONPOSITIONAL0.01
101BH624X-RAY DIFFRACTIONPOSITIONAL
102AZ624X-RAY DIFFRACTIONPOSITIONAL0.009
111BN522X-RAY DIFFRACTIONPOSITIONAL
112AO522X-RAY DIFFRACTIONPOSITIONAL0.008
121BQ417X-RAY DIFFRACTIONPOSITIONAL
122AJ417X-RAY DIFFRACTIONPOSITIONAL0.047
131BP358X-RAY DIFFRACTIONPOSITIONAL
132AX358X-RAY DIFFRACTIONPOSITIONAL0.003
141BR260X-RAY DIFFRACTIONPOSITIONAL
142AC260X-RAY DIFFRACTIONPOSITIONAL0.002
151BS315X-RAY DIFFRACTIONPOSITIONAL
152AD315X-RAY DIFFRACTIONPOSITIONAL0.009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3226-4.4770.35142120.32113504X-RAY DIFFRACTION51
4.477-4.65610.3542840.31265445X-RAY DIFFRACTION79
4.6561-4.86780.31482970.30955732X-RAY DIFFRACTION82
4.8678-5.12420.31113270.30625999X-RAY DIFFRACTION87
5.1242-5.44490.31623850.31436414X-RAY DIFFRACTION93
5.4449-5.86480.33923370.32676792X-RAY DIFFRACTION97
5.8648-6.45390.35683790.31796864X-RAY DIFFRACTION99
6.4539-7.38530.31573420.30276933X-RAY DIFFRACTION99
7.3853-9.29510.26583550.24476965X-RAY DIFFRACTION99
9.2951-50.42690.28583830.26777008X-RAY DIFFRACTION99
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)
11.35840.0403-0.13920.91480.12521.50380.0305-0.0349-0.0433-0.0366-0.05130.3408-0.0983-0.2139-01.5006-0.0042-0.0071.44370.09271.559342.011-43.149368.9673
20.70640.0699-0.47710.8322-0.04451.77480.0921-0.20610.06170.41810.01430.31070.0054-0.071201.5067-0.1038-0.03721.55430.04921.66743.9988-43.8232101.5206
31.2213-0.0237-0.96192.06940.16331.8123-0.0233-0.01710.3187-0.35370.03530.4449-0.5345-0.353801.5281-0.0516-0.45521.6560.02241.797230.0158-17.853662.6283
41.99850.1367-1.62220.1815-0.54794.3229-0.4284-0.4894-0.3818-0.04-0.1616-0.3421.48391.4891-0.46920.46760.2796-0.76072.66410.18721.958194.8903-54.024886.0494
50.6858-0.90480.28141.5069-0.60420.7210.17320.5806-0.581-1.02980.33331.11420.221-0.804402.9581-0.3298-0.22082.4073-0.01882.614915.763-88.56629.2302
60.67520.3852-0.26310.2301-0.11630.0963-0.62510.4357-0.8834-3.22060.5048-0.3162-0.5119-0.8071-0.00023.8137-0.1629-0.18112.69390.00642.777810.961-83.761215.9719
70.62620.09690.38140.21650.35640.5951-0.0140.06520.4426-0.30260.4126-1.0032-2.06961.48550.00011.773-0.27690.12112.8080.03812.174492.3904-13.22550.2137
80.4145-0.31920.32960.3337-0.33180.46110.41020.4140.1136-0.0424-0.06710.6927-1.3827-0.2790.00011.80720.0672-0.46981.77510.0761.836323.1663-23.26742.2332
91.4671.8831-0.0862.4288-0.03630.80390.24841.06680.1371-1.1093-0.7668-0.33910.32030.635502.1974-0.23330.17691.68830.04021.471449.3605-51.802937.4205
100.4632-0.3079-0.38671.55080.0350.4193-0.69040.4385-1.2506-0.60760.5981-0.6863-0.21240.2518-0.00011.1579-0.0954-0.00062.369-0.14532.211293.8774-52.950159.5472
110.2119-0.01170.19760.003-0.14770.46320.2641-0.4716-0.35111.9552-0.1298-0.69680.27611.9103-0.00191.3707-0.1128-0.38972.46240.22732.467784.1866-50.5138103.4581
121.2075-0.4980.16860.2910.2061.2464-0.8518-0.5955-1.0641.6919-0.21570.5550.65010.7433-0.07732.71720.2070.07591.920.35192.006162.1152-80.2832106.9701
130.05070.0104-0.0008-0.05830.04830.080.15450.72460.07440.4322-0.23730.3105-1.1804-0.8527-0.00012.663-0.0299-0.34132.42550.3313.69855.9985-29.75538.4801
141.243-0.0649-0.07751.14660.05681.6694-0.14580.1163-0.0888-0.14530.06940.4601-0.0785-0.2074-02.05890.04370.13931.47190.09781.626851.150744.103431.2622
150.6448-0.1564-0.13140.9156-0.36531.7850.04840.12920.0034-0.39250.03380.106-0.02930.133101.96290.00080.14511.55040.05511.673967.745344.77163.3394
160.4755-0.23270.37141.19860.38972.15480.03760.2293-0.1837-0.180.01240.39020.4456-0.2925-02.02860.01360.30881.70430.13692.240637.685318.695831.1825
170.54470.46410.3540.28870.1191.29880.0543-0.22080.27970.7414-0.1912-0.3979-0.5561.408302.1663-0.3107-0.02572.75990.20882.2654105.800655.181741.2259
180.91220.6306-0.20970.84740.26290.3396-0.4249-0.24830.2071.01520.48521.59760.0861-1.15670.00012.83950.30220.28212.64870.20942.82189.814289.436754.0602
190.3372-0.34470.18840.4734-0.41120.4294-0.6234-0.26130.65362.27820.86431.3859-0.3433-1.0966-0.00023.8140.20650.78622.68350.14053.7647-0.751684.495263.091
200.41410.3239-0.03490.35840.22540.2307-0.6299-0.7825-0.71230.16050.2245-0.66961.82630.9023-0.00012.63450.381-0.02672.59930.03752.069987.385414.159671.6405
210.79350.1484-0.21670.10080.10450.2881-0.0083-0.3188-0.4535-0.1129-0.31360.61490.6849-0.9921-0.00032.5864-0.10120.49071.8960.12132.278322.357224.054745.9926
221.0075-1.47730.71422.3242-1.32721.29630.1807-1.2728-0.4729-0.0626-0.7025-0.152-0.38010.1187-0.00012.63310.13830.33371.605-0.02511.366343.357552.694162.6558
230.41790.550.37990.60210.41230.4713-0.2232-0.22390.28411.0553-0.0942-0.3336-0.30970.0594-02.1513-0.0099-0.37212.33760.06592.184692.924753.955864.18
240.35290.20010.0580.14190.14050.1605-0.40550.64650.13830.3844-0.1885-0.569-0.3931.7861-0.00052.24450.0790.3962.55730.46312.5165104.179751.510120.8447
250.7390.1592-0.25420.1539-0.16830.1538-0.44020.1486-0.5563-1.29710.3479-0.6286-0.50510.1570.00022.7914-0.46140.43612.02140.13192.219186.208981.16596.9988
260.19430.0712-0.0167-0.01390.00360.0274-0.5995-0.1423-0.6814-1.07771.19411.2529-0.1-1.3291-0.00082.5776-0.46320.4042.90.21733.81325.202730.932842.277
270.03480.22510.18340.77850.46061.53550.1928-0.21781.64220.113-0.41590.3103-0.2731-0.292902.4403-0.07490.20183.1542-0.12573.314312.3379-26.636376.897
281.1491-0.3341-1.22990.5728-0.23551.57541.32190.76540.04010.3277-0.54481.06150.1105-0.3031-03.27430.3791-0.36512.9908-0.01183.744930.751829.411310.7368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN BA
2X-RAY DIFFRACTION2CHAIN BB
3X-RAY DIFFRACTION3CHAIN BC
4X-RAY DIFFRACTION4CHAIN BD
5X-RAY DIFFRACTION5CHAIN BE
6X-RAY DIFFRACTION6CHAIN BF
7X-RAY DIFFRACTION7CHAIN BG
8X-RAY DIFFRACTION8CHAIN BH
9X-RAY DIFFRACTION9CHAIN BK
10X-RAY DIFFRACTION10CHAIN BL
11X-RAY DIFFRACTION11CHAIN BN
12X-RAY DIFFRACTION12CHAIN BP
13X-RAY DIFFRACTION13CHAIN BQ
14X-RAY DIFFRACTION14CHAIN AW
15X-RAY DIFFRACTION15CHAIN AR
16X-RAY DIFFRACTION16CHAIN AY
17X-RAY DIFFRACTION17CHAIN AS
18X-RAY DIFFRACTION18CHAIN AT
19X-RAY DIFFRACTION19CHAIN AU
20X-RAY DIFFRACTION20CHAIN AV
21X-RAY DIFFRACTION21CHAIN AZ
22X-RAY DIFFRACTION22CHAIN AI
23X-RAY DIFFRACTION23CHAIN AM
24X-RAY DIFFRACTION24CHAIN AO
25X-RAY DIFFRACTION25CHAIN AX
26X-RAY DIFFRACTION26CHAIN AJ
27X-RAY DIFFRACTION27CHAIN BC OR CHAIN AR
28X-RAY DIFFRACTION28CHAIN BD OR CHAIN AS

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