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- PDB-1qyp: THERMOCOCCUS CELER RPB9, NMR, 25 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1qyp
TitleTHERMOCOCCUS CELER RPB9, NMR, 25 STRUCTURES
ComponentsRNA POLYMERASE II
KeywordsTRANSCRIPTION / RNA POLYMERASE II SUBUNIT / RPB9 / ZN RIBBON / HYPERTHERMOPHILIC / EXTREMOPHILE
Function / homology
Function and homology information


DNA-directed RNA polymerase activity / DNA-directed RNA polymerase complex / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
Transcription factor S / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Zinc finger TFIIS-type signature. / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S ...Transcription factor S / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Zinc finger TFIIS-type signature. / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Transcription factor S
Similarity search - Component
Biological speciesThermococcus celer (archaea)
MethodSOLUTION NMR
AuthorsWang, B. / Jones, D.N.M. / Kaine, B.P. / Weiss, M.A.
Citation
Journal: Structure / Year: 1998
Title: High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases.
Authors: Wang, B. / Jones, D.N. / Kaine, B.P. / Weiss, M.A.
#1: Journal: Nature / Year: 1995
Title: Erratum. Structure of a New Nucleic-Acid-Binding Motif in Eukaryotic Transcriptional Elongation Factor Tfiis
Authors: Qian, X. / Jeon, C. / Yoon, H. / Agarwal, K. / Weiss, M.A.
#2: Journal: Nature / Year: 1993
Title: Structure of a New Nucleic-Acid-Binding Motif in Eukaryotic Transcriptional Elongation Factor Tfiis
Authors: Qian, X. / Jeon, C. / Yoon, H. / Agarwal, K. / Weiss, M.A.
History
DepositionAug 19, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: RNA POLYMERASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7082
Polymers6,6421
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / -
Representative

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Components

#1: Protein RNA POLYMERASE II


Mass: 6642.467 Da / Num. of mol.: 1 / Fragment: SUBUNIT RPB9, C-TERMINAL DOMAIN, RESIDUES 58 -110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus celer (archaea) / Cell line: BL21 / Plasmid: PET15-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS / References: UniProt: Q56254
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionspH: 6 / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

Software
NameClassification
VNMRmodel building
X-PLORmodel building
X-PLORrefinement
VNMRphasing
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 25

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