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- PDB-2y0s: Crystal structure of Sulfolobus shibatae RNA polymerase in P21 sp... -

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Basic information

Entry
Database: PDB / ID: 2y0s
TitleCrystal structure of Sulfolobus shibatae RNA polymerase in P21 space group
Components
  • (DNA-DIRECTED RNA ...) x 8
  • (RNA POLYMERASE SUBUNIT ...) x 5
KeywordsTRANSFERASE / NUCLEOTIDYLTRANSFERASE / TRANSCRIPTION / METAL-BINDING
Function / homology
Function and homology information


3 iron, 4 sulfur cluster binding / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / nucleic acid binding / protein dimerization activity / molecular adaptor activity ...3 iron, 4 sulfur cluster binding / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / nucleic acid binding / protein dimerization activity / molecular adaptor activity / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / DNA polymerase; domain 1 - #390 / RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 ...Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / DNA polymerase; domain 1 - #390 / RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 / Dihydrolipoamide Transferase / HRDC domain / RNA polymerase ii / RNA polymerase Rpb1 funnel domain / N-terminal domain of TfIIb / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / Alpha-Beta Plaits - #20 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / Other non-globular / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Rubrerythrin, domain 2 / Helix Hairpins / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Gyrase A; domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / HRDC-like superfamily / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerases L / 13 to 16 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Homeodomain-like / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Single Sheet / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Beta Complex / Helix non-globular / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, clamp domain superfamily
Similarity search - Domain/homology
FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 ...FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo13
Similarity search - Component
Biological speciesSULFOLOBUS SHIBATAE (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsWojtas, M. / Peralta, B. / Ondiviela, M. / Mogni, M. / Bell, S.D. / Abrescia, N.G.A.
Citation
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.
#1: 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.
History
DepositionDec 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Derived calculations / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Oct 30, 2019Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" 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. THE SHEETS PRESENTED AS "BM" 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. THE SHEETS PRESENTED AS "RM" 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. THE SHEETS PRESENTED AS "WB" 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
A: DNA-DIRECTED RNA POLYMERASE
B: DNA-DIRECTED RNA POLYMERASE
C: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
D: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
E: RNA POLYMERASE SUBUNIT 4
F: RNA POLYMERASE SUBUNIT 7
G: RNA POLYMERASE SUBUNIT 8
H: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
I: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
J: RNA POLYMERASE SUBUNIT 13
K: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
L: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
M: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
N: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
O: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
P: RNA POLYMERASE SUBUNIT 12
Q: RNA POLYMERASE SUBUNIT 13
R: DNA-DIRECTED RNA POLYMERASE
S: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
T: RNA POLYMERASE SUBUNIT 4
U: RNA POLYMERASE SUBUNIT 7
V: RNA POLYMERASE SUBUNIT 8
W: DNA-DIRECTED RNA POLYMERASE
X: RNA POLYMERASE SUBUNIT 12
Y: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
Z: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)812,82544
Polymers811,26926
Non-polymers1,55618
Water0
1
K: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
M: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
O: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
Q: RNA POLYMERASE SUBUNIT 13
R: DNA-DIRECTED RNA POLYMERASE
S: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
T: RNA POLYMERASE SUBUNIT 4
U: RNA POLYMERASE SUBUNIT 7
V: RNA POLYMERASE SUBUNIT 8
W: DNA-DIRECTED RNA POLYMERASE
X: RNA POLYMERASE SUBUNIT 12
Y: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
Z: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,41222
Polymers405,63513
Non-polymers7789
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area61460 Å2
ΔGint-381.2 kcal/mol
Surface area173340 Å2
MethodPISA
2
A: DNA-DIRECTED RNA POLYMERASE
B: DNA-DIRECTED RNA POLYMERASE
C: DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
D: DNA-DIRECTED RNA POLYMERASE SUBUNIT D
E: RNA POLYMERASE SUBUNIT 4
F: RNA POLYMERASE SUBUNIT 7
G: RNA POLYMERASE SUBUNIT 8
H: DNA-DIRECTED RNA POLYMERASE SUBUNIT H
I: DNA-DIRECTED RNA POLYMERASE SUBUNIT K
J: RNA POLYMERASE SUBUNIT 13
L: DNA-DIRECTED RNA POLYMERASE SUBUNIT L
N: DNA-DIRECTED RNA POLYMERASE SUBUNIT N
P: RNA POLYMERASE SUBUNIT 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,41222
Polymers405,63513
Non-polymers7789
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area63020 Å2
ΔGint-387.9 kcal/mol
Surface area180640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.330, 195.909, 212.451
Angle α, β, γ (deg.)90.00, 105.73, 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

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 8:196 OR RESSEQ 202:507 OR RESSEQ...
211CHAIN R AND (RESSEQ 8:196 OR RESSEQ 202:507 OR RESSEQ...
112CHAIN A AND (RESSEQ 4:30 OR RESSEQ 45:151 OR RESSEQ 175:224 OR RESSEQ 233:879 ) AND (NOT ELEMENT H)
212CHAIN W AND (RESSEQ 4:30 OR RESSEQ 45:151 OR RESSEQ 175:224 OR RESSEQ 233:879 ) AND (NOT ELEMENT H)
113CHAIN C AND (RESSEQ 11:84 OR RESSEQ 102:395 ) AND (NOT ELEMENT H)
213CHAIN Y AND (RESSEQ 11:84 OR RESSEQ 102:395 ) AND (NOT ELEMENT H)
114CHAIN D AND (RESSEQ 2:85 OR RESSEQ 89:264 ) AND (NOT ELEMENT H)
214CHAIN S AND (RESSEQ 2:85 OR RESSEQ 89:264 ) AND (NOT ELEMENT H)
115CHAIN E AND (RESSEQ 1:151 OR RESSEQ 158:170 ) AND (NOT ELEMENT H)
215CHAIN T AND (RESSEQ 1:151 OR RESSEQ 158:170 ) AND (NOT ELEMENT H)
116CHAIN G AND (RESSEQ 7:116 ) AND (NOT ELEMENT H)
216CHAIN V AND (RESSEQ 7:116 ) AND (NOT ELEMENT H)
117CHAIN L AND (RESSEQ 1:91 ) AND (NOT ELEMENT H)
217CHAIN M AND (RESSEQ 1:91 ) AND (NOT ELEMENT H)
118CHAIN F AND (RESSEQ 3:92 ) AND (NOT ELEMENT H)
218CHAIN U AND (RESSEQ 3:92 ) AND (NOT ELEMENT H)
119CHAIN K AND (RESSEQ 11:92 ) AND (NOT ELEMENT H)
219CHAIN I AND (RESSEQ 11:92 ) AND (NOT ELEMENT H)
1110CHAIN H AND (RESSEQ 9:82 ) AND (NOT ELEMENT H)
2110CHAIN Z AND (RESSEQ 9:82 ) AND (NOT ELEMENT H)
1111CHAIN N AND (RESSEQ 1:64 ) AND (NOT ELEMENT H)
2111CHAIN O AND (RESSEQ 1:64 ) AND (NOT ELEMENT H)
1112CHAIN Q AND (RESSEQ 39:77 ) AND (NOT ELEMENT H)
2112CHAIN J AND (RESSEQ 39:77 ) AND (NOT ELEMENT H)
1113CHAIN P AND (RESSEQ 6:48 ) AND (NOT ELEMENT H)
2113CHAIN X AND (RESSEQ 6:48 ) AND (NOT ELEMENT H)

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

NCS oper: (Code: given
Matrix: (0.8546, -0.001801, 0.5193), (-0.002106, -1, -2.2E-5), (0.5193, -0.001092, -0.8546)
Vector: -28.42, 0.6494, 102.3)

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Components

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DNA-DIRECTED RNA ... , 8 types, 16 molecules AWBRCYDSHZIKLMNO

#1: Protein DNA-DIRECTED RNA POLYMERASE / Polymerase


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


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


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


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


Mass: 9688.296 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB60, DNA-directed RNA polymerase
#9: Protein DNA-DIRECTED RNA POLYMERASE SUBUNIT K / Polymerase


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


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


Mass: 7617.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB63, DNA-directed RNA polymerase

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RNA POLYMERASE SUBUNIT ... , 5 types, 10 molecules ETFUGVJQPX

#5: Protein RNA POLYMERASE SUBUNIT 4 /


Mass: 20328.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB57, DNA-directed RNA polymerase
#6: Protein RNA POLYMERASE SUBUNIT 7 /


Mass: 12822.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RPO4 / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB58
#7: Protein RNA POLYMERASE SUBUNIT 8 /


Mass: 15139.458 Da / Num. of mol.: 2 / Fragment: RPO8 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB59
#10: Protein RNA POLYMERASE SUBUNIT 13 /


Mass: 12169.592 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB65
#13: Protein/peptide RNA POLYMERASE SUBUNIT 12 /


Mass: 5606.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB64

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Non-polymers , 3 types, 18 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4

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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: 3.45 Å3/Da / Density % sol: 64.4 % / Description: NONE
Crystal growpH: 7.8 / Details: pH 7.8

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSLS X06DA11
SYNCHROTRONESRF ID14-120.9334
Detector
TypeIDDetectorDate
MARRESEARCH1CCDNov 6, 2009
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.93341
ReflectionResolution: 3.79→50 Å / Num. obs: 100163 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 79.35 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.1
Reflection shellResolution: 3.79→3.99 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.1 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WAQ

2waq


Resolution: 3.8→29.858 Å / SU ML: 0.55 / σ(F): 1.34 / Phase error: 36.85 / Stereochemistry target values: ML
Details: DURING REFINEMENT IN PHENIX THE STRUCTURE-DIHEDRALS WERE RESTRAINED AGAINST THE 2WAQ. THE STATS PROVIDED INCLUDE THE RIDING HS DURING REFINEMENT THAT HAVE BEEN REMOVED FROM THE SUBMITTED ...Details: DURING REFINEMENT IN PHENIX THE STRUCTURE-DIHEDRALS WERE RESTRAINED AGAINST THE 2WAQ. THE STATS PROVIDED INCLUDE THE RIDING HS DURING REFINEMENT THAT HAVE BEEN REMOVED FROM THE SUBMITTED COORDINATES TO FULFILL THE ATOMS LIMITATION OF 99999 OF THE PDB FORMAT.
RfactorNum. reflection% reflection
Rfree0.3539 4959 5 %
Rwork0.2997 --
obs0.3024 99215 99.16 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT / Bsol: 71.911 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 135.7 Å2
Baniso -1Baniso -2Baniso -3
1-17.0982 Å20 Å218.7796 Å2
2---6.959 Å2-0 Å2
3----10.1392 Å2
Refinement stepCycle: LAST / Resolution: 3.8→29.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52442 0 30 0 52472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01653497
X-RAY DIFFRACTIONf_angle_d1.51472248
X-RAY DIFFRACTIONf_dihedral_angle_d15.15820486
X-RAY DIFFRACTIONf_chiral_restr0.0788242
X-RAY DIFFRACTIONf_plane_restr0.0079242
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B8622X-RAY DIFFRACTIONPOSITIONAL
12R8622X-RAY DIFFRACTIONPOSITIONAL0.039
21A6620X-RAY DIFFRACTIONPOSITIONAL
22W6620X-RAY DIFFRACTIONPOSITIONAL0.059
31C2844X-RAY DIFFRACTIONPOSITIONAL
32Y2844X-RAY DIFFRACTIONPOSITIONAL0.035
41D2071X-RAY DIFFRACTIONPOSITIONAL
42S2071X-RAY DIFFRACTIONPOSITIONAL0.03
51E1298X-RAY DIFFRACTIONPOSITIONAL
52T1298X-RAY DIFFRACTIONPOSITIONAL0.031
61G878X-RAY DIFFRACTIONPOSITIONAL
62V878X-RAY DIFFRACTIONPOSITIONAL0.028
71L707X-RAY DIFFRACTIONPOSITIONAL
72M707X-RAY DIFFRACTIONPOSITIONAL0.031
81F701X-RAY DIFFRACTIONPOSITIONAL
82U701X-RAY DIFFRACTIONPOSITIONAL0.025
91K658X-RAY DIFFRACTIONPOSITIONAL
92I658X-RAY DIFFRACTIONPOSITIONAL0.04
101H609X-RAY DIFFRACTIONPOSITIONAL
102Z609X-RAY DIFFRACTIONPOSITIONAL0.034
111N514X-RAY DIFFRACTIONPOSITIONAL
112O514X-RAY DIFFRACTIONPOSITIONAL0.074
121Q332X-RAY DIFFRACTIONPOSITIONAL
122J332X-RAY DIFFRACTIONPOSITIONAL0.027
131P346X-RAY DIFFRACTIONPOSITIONAL
132X346X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.84310.38011500.34133030X-RAY DIFFRACTION96
3.8431-3.88820.43071650.37682993X-RAY DIFFRACTION96
3.8882-3.93550.45741780.41993052X-RAY DIFFRACTION96
3.9355-3.98520.35181430.33873059X-RAY DIFFRACTION97
3.9852-4.03760.35211550.30293113X-RAY DIFFRACTION97
4.0376-4.09270.31611650.30133107X-RAY DIFFRACTION99
4.0927-4.15110.36451720.29713064X-RAY DIFFRACTION99
4.1511-4.21280.38331550.28763161X-RAY DIFFRACTION99
4.2128-4.27850.33671640.28563141X-RAY DIFFRACTION99
4.2785-4.34840.31831670.27823161X-RAY DIFFRACTION100
4.3484-4.42320.30851750.26823151X-RAY DIFFRACTION100
4.4232-4.50330.32231700.26613135X-RAY DIFFRACTION100
4.5033-4.58970.32721630.26713152X-RAY DIFFRACTION100
4.5897-4.6830.31631800.25343155X-RAY DIFFRACTION100
4.683-4.78440.29561850.2663148X-RAY DIFFRACTION100
4.7844-4.89520.33071350.27863184X-RAY DIFFRACTION100
4.8952-5.01710.36051650.28663146X-RAY DIFFRACTION100
5.0171-5.15210.3191580.2993180X-RAY DIFFRACTION100
5.1521-5.30290.38391560.30033174X-RAY DIFFRACTION100
5.3029-5.4730.381740.32293140X-RAY DIFFRACTION100
5.473-5.66740.40821630.33183182X-RAY DIFFRACTION100
5.6674-5.89260.41111590.33733214X-RAY DIFFRACTION100
5.8926-6.15860.42121680.33623165X-RAY DIFFRACTION100
6.1586-6.48020.39391710.33433149X-RAY DIFFRACTION100
6.4802-6.88150.37631560.32173185X-RAY DIFFRACTION100
6.8815-7.40530.3921700.29483147X-RAY DIFFRACTION100
7.4053-8.13690.34451700.27473216X-RAY DIFFRACTION100
8.1369-9.28320.30591690.25973187X-RAY DIFFRACTION100
9.2832-11.58120.29891750.24993171X-RAY DIFFRACTION99
11.5812-29.85860.37731830.34873192X-RAY DIFFRACTION99
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)
1-0.14760.135-0.06510.2786-0.07440.1401-0.1551-0.2376-0.0443-0.5163-0.2172-0.07750.0853-0.0038-0.2167-0.05070.0977-0.040.8134-0.05881.01332.4017-57.888432.3977
2-0.1961-0.0311-0.18230.10690.02740.1629-0.05620.1026-0.08570.12680.0227-0.1706-0.0767-0.20150.00370.17250.04750.01290.3809-0.0690.4183-22.409-37.496236.8474
30.1490.2041-0.3222-0.0811-0.4555-0.0342-0.0168-0.05050.0193-0.0162-0.02710.0686-0.10.1548-0.08210.3726-0.0455-0.05270.3661-0.22370.2518-6.8477-25.831832.1707
40.1485-0.22170.1466-0.29240.06680.12660.1194-0.29760.2606-0.3735-0.06020.02710.2524-0.01960.00060.7340.06980.04240.4240.01590.3067-0.463-52.6675-15.6053
50.0001-0.0840.00940.11070.05450.06720.12830.0319-0.24360.0557-0.08440.0811-0.17820.0593-00.4223-0.16190.36940.8282-0.05441.252728.7579-23.9903-4.395
6-0.1287-0.01050.05490.07110.123-0.00440.1039-0.1342-0.0704-0.1319-0.0496-0.108-0.0563-0.11150.00260.32210.0188-0.01080.3610.02980.4382-9.2768-45.4227.6881
70.51720.3764-0.29990.3983-0.10350.130.0160.1207-0.51580.1642-0.295-0.528-0.4017-0.2986-0.27470.4084-0.0422-0.31250.4315-0.04830.2106-7.55-22.030157.0288
80.159-0.1669-0.0660.22380.2770.2626-0.12990.1895-0.56120.0942-0.31850.102-0.313-0.0299-0.25460.4114-0.1009-0.28440.090.27410.560325.05722.01622.4028
90.03290.46410.15170.35970.19530.10650.03810.074-0.17080.16330.02290.0325-0.2560.09220.01360.2782-0.109-0.03910.26690.02910.648510.5528-32.558446.1699
10-0.0013-0.1817-0.1290.00810.0930.2316-0.1357-0.10960.3037-0.21090.34960.04380.69140.2207-0.05010.1018-0.3362-0.24260.9945-0.19420.7493-48.7444-63.705612.5161
11-0.2158-0.2317-0.29390.498-0.34920.96390.1760.3103-0.35760.388-0.4526-0.5204-0.4988-0.7549-0.08820.0590.2285-0.07331.41220.11861.0985-58.1954-37.38923.2417
120.0706-0.1121-0.0821-0.0039-0.02810.15250.23720.45430.03420.6133-0.0303-0.10020.135-0.211301.23420.2846-0.12510.83010.23370.70327.2662-73.592771.7878
13-0.0126-0.01380.00260.00190.04690.0936-0.2078-0.2689-0.1595-0.2132-0.2663-0.0265-0.0593-0.078900.99150.1794-0.31520.6979-0.09871.663934.9094-99.109275.2421
140.0527-0.0394-0.04410.0066-0.00420.0055-0.0970.08780.12960.1137-0.19770.19260.06240.1738-01.1860.4046-0.09570.8918-0.02171.027616.016-85.40981.7414
150.03140.00530.0240.01230.0066-0.0039-0.28120.2126-0.12210.19290.10210.1625-0.17550.207701.27040.5805-0.64011.4729-0.22231.545132.742-81.331690.2316
160.33270.15250.44840.07150.17671.453-0.4086-0.1078-0.4628-0.18970.01420.0709-0.67570.116-0.12190.45530.64470.20911.04570.02030.8664-50.8306-12.469951.86
170.0452-0.044-0.04340.06050.04760.0442-0.0323-0.553-0.1271-0.5671-0.0430.138-0.17710.140700.81990.0432-0.09730.630.10850.551616.0118-23.429661.2122
180.70420.04510.08070.5320.2391-0.1549-0.15960.62080.27230.61560.5526-0.11040.31120.04980.22980.64010.16210.01430.32520.17490.1555-9.6494-50.932365.2257
190.4205-0.04410.2637-0.1448-0.09680.0338-1.15870.1071-0.04330.516-0.0490.2573-0.11910.2618-0.3518-0.0239-0.18450.04081.12990.06391.0356-52.4435-51.924143.0054
20-0.0184-0.1141-0.11830.2934-0.1840.14240.2460.12820.05930.3630.72630.1905-0.9-0.49240.8549-0.2559-0.4373-0.60290.9344-0.34250.5524-41.7889-49.2568-0.0932
210.1247-0.11070.16670.0533-0.08780.13720.0424-0.5694-0.3504-0.75920.0349-0.0322-0.2073-0.1858-00.8962-0.0762-0.07610.8229-0.320.9492-20.1672-78.9961-3.2582
22-0.0105-0.0121-0.0162-0.00150.0087-0.0005-0.1563-0.1766-0.172-0.104-0.0838-0.1586-0.1032-0.103-00.78450.2912-0.71021.1375-0.15461.696532.0157-31.475567.3982
230.11280.1426-0.02250.1187-0.11880.0124-0.10750.1643-0.28660.2203-0.10980.1626-0.20140.192601.22450.0241-0.11351.0783-0.09691.143415.900958.50891.2333
24-0.23630.0703-0.04690.17970.07910.2848-0.0960.0102-0.08320.0002-0.0031-0.304-0.108-0.334-0.00010.8832-0.06790.05240.4722-0.09250.3812-28.765338.212359.0944
25-0.03720.11480.02830.0726-0.36140.13020.0159-0.0955-0.2161-0.0433-0.1042-0.0837-0.1882-0.029601.10950.02530.19980.652-0.13220.682-17.88926.523971.1429
260.20240.3368-0.1538-0.19750.10780.14430.19270.13280.04830.23330.0095-0.00050.0791-0.109300.92850.02280.1470.6664-0.0570.5766-37.356953.3594115.3252
270.05660.0686-0.03850.09780.10630.0645-0.46-0.06680.2195-0.0628-0.0585-0.01450.2410.0271-0.00081.03250.2452-0.40810.59920.13830.8233-6.638424.6143120.9662
28-0.1351-0.0818-0.22860.03040.22730.10680.02270.10070.09280.1094-0.0758-0.14210.0605-0.1433-00.9405-0.02690.00790.64010.04680.654-32.758746.11790.8481
290.2345-0.13790.1550.12730.08740.1175-0.1770.16220.16220.1313-0.1717-0.24230.3361-0.11601.11260.00310.46320.703-0.05211.0446-5.595722.730449.5813
300.02490.0132-0.02740.03060.24850.1252-0.198-0.11590.0456-0.0802-0.27310.06910.00320.019800.68330.04480.21270.36120.39961.12584.2811-1.316596.1059
310.2062-0.37090.05830.2062-0.1014-0.0907-0.1776-0.05820.0501-0.05570.0467-0.07420.0803-0.011901.03380.05460.06250.29110.0560.81114.309933.236768.2339
320.09850.06530.0201-0.02330.0408-0.02820.0108-0.0228-0.1011-0.04220.5174-0.0987-0.1779-0.1745-01.00930.3953-0.12841.2193-0.06110.7319-63.885864.485666.2799
33-0.05020.0354-0.01830.0504-0.036-0.06910.06190.1725-0.24040.1113-0.8243-0.6553-0.2239-0.7962-0.00020.9283-0.1319-0.32351.6201-0.11180.7485-66.497638.204852.1582
340.01890.03320.0422-0.02-0.05560.09410.05950.0750.28510.01630.0187-0.05460.3034-0.051801.4226-0.32330.44880.681-0.01020.713214.797674.275644.5818
350.0358-0.014-0.0577-0.00640.02440.0749-0.16330.20890.17920.0725-0.4374-0.00960.05220.064200.9726-0.0878-0.30321.0536-0.07361.769540.348399.66155.9795
36-0.01480.01680.00270.03050.05540.04640.2243-0.21950.188-0.203-0.07410.27770.24460.2901-01.6324-0.30190.01691.11-0.14551.538927.542186.008340.569
370.02860.01270.00190.00140.0019-0.006-0.2086-0.1856-0.0595-0.09180.05830.0498-0.04490.046501.1801-0.42240.2831.7881-0.44242.073746.23381.851841.9229
380.1145-0.117-0.01380.1102-0.11840.0807-0.50540.2637-0.03070.1504-0.19270.07630.02090.053901.0734-0.4712-0.07741.1488-0.21510.6411-45.315613.229331.5281
390.0943-0.02020.05470.03480.04750.0616-0.01830.0723-0.03980.0704-0.13890.3887-0.06150.409701.1482-0.03960.31350.95540.11051.076216.759124.04658.1777
400.16370.04240.14860.05920.05750.01270.2974-0.3693-0.4126-0.40850.1948-0.1724-0.4418-0.15730.00011.2715-0.1950.27240.36760.04350.4983-3.141851.59541.4703
410.0043-0.0267-0.0090.0492-0.11280.0598-0.3343-0.3148-0.1263-0.3465-0.12790.2224-0.28050.229901.5110.141-0.30721.39220.22260.7437-51.250252.626538.2357
42-0.06110.04920.04560.00370.14630.1392-0.8492-0.1880.1037-0.0906-0.1406-0.12260.1932-0.1194-0.00690.73180.3798-0.12971.5675-0.29561.1841-64.511949.986880.626
430.17580.0221-0.07850.05960.01970.0404-0.11410.27890.18640.2773-0.09850.3030.01340.107301.44550.33950.06670.8489-0.16570.9675-47.603479.689294.5481
44-0.01460.01870.01310.00760.0021-0.0003-0.0505-0.0248-0.1516-0.01150.1156-0.0961-0.017-0.011500.64490.05510.27931.4101-0.25772.272633.766732.160361.1061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 4:298
2X-RAY DIFFRACTION2CHAIN A AND RESID 299:755
3X-RAY DIFFRACTION3CHAIN A AND RESID 756:879
4X-RAY DIFFRACTION4CHAIN B AND RESID 8:174
5X-RAY DIFFRACTION5CHAIN B AND RESID 175:334
6X-RAY DIFFRACTION6CHAIN B AND RESID 335:1122
7X-RAY DIFFRACTION7CHAIN C AND RESID 11:125
8X-RAY DIFFRACTION8CHAIN C AND RESID 126:249
9X-RAY DIFFRACTION9CHAIN C AND RESID 250:395
10X-RAY DIFFRACTION10CHAIN D AND RESID 2:157
11X-RAY DIFFRACTION11CHAIN D AND RESID 158:264
12X-RAY DIFFRACTION12CHAIN E AND RESID 1:78
13X-RAY DIFFRACTION13CHAIN E AND RESID 79:177
14X-RAY DIFFRACTION14CHAIN F AND RESID 3:46
15X-RAY DIFFRACTION15CHAIN F AND RESID 47:92
16X-RAY DIFFRACTION16CHAIN G
17X-RAY DIFFRACTION17CHAIN H
18X-RAY DIFFRACTION18CHAIN K
19X-RAY DIFFRACTION19CHAIN L
20X-RAY DIFFRACTION20CHAIN N AND RESID 1:64
21X-RAY DIFFRACTION21CHAIN P AND RESID 4:48
22X-RAY DIFFRACTION22CHAIN Q
23X-RAY DIFFRACTION23CHAIN W AND RESID 4:298
24X-RAY DIFFRACTION24CHAIN W AND RESID 299:755
25X-RAY DIFFRACTION25CHAIN W AND RESID 756:879
26X-RAY DIFFRACTION26CHAIN R AND RESID 8:174
27X-RAY DIFFRACTION27CHAIN R AND RESID 175:334
28X-RAY DIFFRACTION28CHAIN R AND RESID 335:1122
29X-RAY DIFFRACTION29CHAIN Y AND RESID 11:125
30X-RAY DIFFRACTION30CHAIN Y AND RESID 126:249
31X-RAY DIFFRACTION31CHAIN Y AND RESID 250:395
32X-RAY DIFFRACTION32CHAIN S AND RESID 2:157
33X-RAY DIFFRACTION33CHAIN S AND RESID 158:264
34X-RAY DIFFRACTION34CHAIN T AND RESID 1:78
35X-RAY DIFFRACTION35CHAIN T AND RESID 79:177
36X-RAY DIFFRACTION36CHAIN U AND RESID 3:46
37X-RAY DIFFRACTION37CHAIN U AND RESID 47:92
38X-RAY DIFFRACTION38CHAIN V
39X-RAY DIFFRACTION39CHAIN Z
40X-RAY DIFFRACTION40CHAIN I
41X-RAY DIFFRACTION41CHAIN M
42X-RAY DIFFRACTION42CHAIN O AND RESID 1:64
43X-RAY DIFFRACTION43CHAIN X AND RESID 4:48
44X-RAY DIFFRACTION44CHAIN J

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