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- PDB-4nc7: N-terminal domain of delta-subunit of RNA polymerase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 4nc7
TitleN-terminal domain of delta-subunit of RNA polymerase complexed with I3C and 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
Chem-I3C / NICKEL (II) ION / DNA-directed RNA polymerase subunit delta
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_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

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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)24,2145
Polymers23,5382
Non-polymers6763
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
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)24,7736
Polymers23,5382
Non-polymers1,2354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2950 Å2
ΔGint-19 kcal/mol
Surface area9460 Å2
MethodPISA
3
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_555-x,y,-z+1/21
Buried area3210 Å2
ΔGint-21 kcal/mol
Surface area9290 Å2
MethodPISA
4
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)48,42910
Polymers47,0764
Non-polymers1,3526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8790 Å2
ΔGint-50 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.650, 110.200, 85.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

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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-I3C / 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid / 5-Amino-2,4,6-triiodoisophthalic acid


Mass: 558.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H4I3NO4
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


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


Mass: 18.015 Da / Num. of mol.: 80 / 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 (%)
12.0840.81
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 diffusion8.21.8M sodium/potassium phosphate, pH 8.2, VAPOR DIFFUSION, temperature 290.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.5419 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 21, 2011
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2→27.5 Å / Num. all: 13668 / Num. obs: 13651 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.11 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
Auto-Rickshawphasing
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→27.5 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.042 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.182 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25937 676 5 %RANDOM
Rwork0.20129 ---
all0.239 13651 --
obs0.20418 12976 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.803 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å20 Å20 Å2
2---2.55 Å2-0 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 2→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 18 80 1412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191379
X-RAY DIFFRACTIONr_bond_other_d0.0010.021294
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9771864
X-RAY DIFFRACTIONr_angle_other_deg0.8932987
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.155160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.09925.20573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89915254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.503156
X-RAY DIFFRACTIONr_chiral_restr0.1070.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021556
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02320
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 59 -
Rwork0.231 937 -
obs--100 %

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