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- PDB-1ef4: SOLUTION STRUCTURE OF THE ESSENTIAL RNA POLYMERASE SUBUNIT RPB10 ... -

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Basic information

Entry
Database: PDB / ID: 1ef4
TitleSOLUTION STRUCTURE OF THE ESSENTIAL RNA POLYMERASE SUBUNIT RPB10 FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
ComponentsDNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE / THREE HELIX BUNDLE / ZINC BINDING / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Homeodomain-like / 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. / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit Rpo10
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / DISTANCE GEOMETRY WITH SIMULATED ANNEALING
AuthorsMackereth, C.D. / Arrowsmith, C.H. / Edwards, A.M. / Mcintosh, L.P. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Zinc-bundle structure of the essential RNA polymerase subunit RPB10 from Methanobacterium thermoautotrophicum.
Authors: Mackereth, C.D. / Arrowsmith, C.H. / Edwards, A.M. / McIntosh, L.P.
History
DepositionFeb 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5102
Polymers6,4441
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 60structures with acceptable covalent geometry
RepresentativeModel #1

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Components

#1: Protein DNA-DIRECTED RNA POLYMERASE / SUBUNIT N


Mass: 6444.494 Da / Num. of mol.: 1 / Fragment: SUBUNIT RPB10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: O26147, DNA-directed RNA polymerase
#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
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D METHYL-METHYL 13C SEPARATED NOESY
1212D NOESY
1313D 13C-SEPARATED NOESY
1413D 15N-SEPARATED NOESY
151HNHA
1612D CT-HMQC-J
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING TRIPLE- RESONANCE NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 0.5MM RPB10 U-15N,13C 20MM DEUTERATED D-TRIS; 0.15M NACL; 2MM BETA- MERCAPTOETHANOL; 99% D2O, 1% H2O
Sample conditionsIonic strength: 150mM_NACL / pH: 7.5 / Pressure: AMBIENT / Temperature: 303.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR 3.851, ARIA1999BRUNGER (X-PLOR), NILGES (ARIA)refinement
VNMR6structure solution
Felix95structure solution
RefinementMethod: DISTANCE GEOMETRY WITH SIMULATED ANNEALING / Software ordinal: 1
Details: REFINED USING ARIA AMBIGUOUS AND UNAMBIGUOUS RESTRAINTS, AND INCLUDING RESTRAINTS FOR DIHEDRAL ANGLES AND HYDROGEN BOND DISTANCES. ZINC COORDINATION TO CYS 6,9,43,44 WITH IDEALIZED ...Details: REFINED USING ARIA AMBIGUOUS AND UNAMBIGUOUS RESTRAINTS, AND INCLUDING RESTRAINTS FOR DIHEDRAL ANGLES AND HYDROGEN BOND DISTANCES. ZINC COORDINATION TO CYS 6,9,43,44 WITH IDEALIZED TETRAHEDRAL RESTRAINTS WERE ADDED IN THE FINAL ROUNDS OF REFINEMENT; THE COORDINATING LIGANDS AND THEIR GEOMETRIC ARRANGEMENT WERE IDENTIFIED BASED ON INITIAL NOE-DERIVED STRUCTURES CALCULATED WITHOUT INCLUSION OF THE METAL ION. THREE N- TERMINAL RESIDUES (GLY-SER-HIS) REMAINING FROM CLEAVAGE OF THE HIS-TAG WERE DISORDERED AND NOT INCLUDED IN THE FINAL ENSEMBLE.
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 60 / Conformers submitted total number: 20

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