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- PDB-4nc8: N-terminal domain of delta-subunit of RNA polymerase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 4nc8
TitleN-terminal domain of delta-subunit of RNA polymerase complexed with nickel ions
ComponentsDNA-directed RNA polymerase subunit deltaPolymerase
KeywordsTRANSCRIPTION / nucleus
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-templated transcription / regulation of DNA-templated transcription
Similarity search - Function
RNA polymerase, subunit delta, N-terminal domain / DNA-directed RNA polymerase subunit delta / DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily / ASXL, HARE-HTH domain / HB1, ASXL, restriction endonuclease HTH domain / HARE-type HTH domain profile. / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / DNA-directed RNA polymerase subunit delta
Similarity search - Component
Biological speciesBacillus Subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsDemo, G. / Papouskova, V. / Komarek, J. / Sanderova, H. / Rabatinova, A. / Krasny, L. / Zidek, L. / Sklenar, V. / Wimmerova, M.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: X-ray vs. NMR structure of N-terminal domain of delta-subunit of RNA polymerase.
Authors: Demo, G. / Papouskova, V. / Komarek, J. / Kaderavek, P. / Otrusinova, O. / Srb, P. / Rabatinova, A. / Krasny, L. / Zidek, L. / Sklenar, V. / Wimmerova, M.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 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_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit delta
B: DNA-directed RNA polymerase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6564
Polymers23,5382
Non-polymers1172
Water36020
1
A: DNA-directed RNA polymerase subunit delta
hetero molecules

A: DNA-directed RNA polymerase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6564
Polymers23,5382
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2980 Å2
ΔGint-21 kcal/mol
Surface area9230 Å2
MethodPISA
2
B: DNA-directed RNA polymerase subunit delta
hetero molecules

B: DNA-directed RNA polymerase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6564
Polymers23,5382
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area2950 Å2
ΔGint-21 kcal/mol
Surface area9400 Å2
MethodPISA
3
A: DNA-directed RNA polymerase subunit delta
B: DNA-directed RNA polymerase subunit delta
hetero molecules

A: DNA-directed RNA polymerase subunit delta
B: DNA-directed RNA polymerase subunit delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3118
Polymers47,0764
Non-polymers2354
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area8540 Å2
ΔGint-53 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.462, 109.636, 82.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DNA-directed RNA polymerase subunit delta / Polymerase / RNAP delta factor


Mass: 11769.083 Da / Num. of mol.: 2 / Fragment: UNP residues 2-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus Subtilis (bacteria) / Strain: 168 / Gene: rpoE, BSU37160 / Production host: Escherichia coli (E. coli) / References: UniProt: P12464
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.9135.44
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
290.151vapor diffusion, hanging drop82M sodium/potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K
290.152vapor diffusion, hanging drop8.21.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9871 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 18, 2012
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9871 Å / Relative weight: 1
ReflectionResolution: 2.16→41.5 Å / Num. all: 9941 / Num. obs: 9786 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.17→2.28 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NC7

4nc7


Resolution: 2.17→41.5 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.945 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.289 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28263 470 4.8 %RANDOM
Rwork0.22391 ---
all0.267 9762 --
obs0.22682 9317 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.528 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å20 Å20 Å2
2---2.62 Å2-0 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.17→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 2 20 1336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191351
X-RAY DIFFRACTIONr_bond_other_d0.0010.021292
X-RAY DIFFRACTIONr_angle_refined_deg1.541.9651821
X-RAY DIFFRACTIONr_angle_other_deg0.78432981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.78825.06873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94515255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.34157
X-RAY DIFFRACTIONr_chiral_restr0.0770.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021510
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
LS refinement shellResolution: 2.17→2.222 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 25 -
Rwork0.315 643 -
obs--92.52 %

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