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- PDB-4qjf: X-ray crystal structure of Thermocuccus kodakarensis RNA polymera... -

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Basic information

Entry
Database: PDB / ID: 4qjf
TitleX-ray crystal structure of Thermocuccus kodakarensis RNA polymerase Rpp4/Rpo7 (RpoF/RpoE) complex
Components
  • DNA-directed RNA polymerase, subunit E'Polymerase
  • DNA-directed RNA polymerase, subunit FPolymerase
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-templated transcription initiation / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / nucleotide binding / DNA binding / cytoplasm
Similarity search - Function
Helix Hairpins - #10 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4 / HRDC domain / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / Helix Hairpins / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 ...Helix Hairpins - #10 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4 / HRDC domain / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / Helix Hairpins / S1 domain profile. / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / 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 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Helix non-globular / Special / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo7
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.312 Å
AuthorsMurakami, K.S.
CitationJournal: Nat.Commun. / Year: 2014
Title: Crystal structure of euryarchaeal RNA polymerase and insight into the evolution of RNA polymerase II structure
Authors: Murakami, K.S.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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 E'
B: DNA-directed RNA polymerase, subunit F


Theoretical massNumber of molelcules
Total (without water)36,4132
Polymers36,4132
Non-polymers00
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-16 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.465, 80.942, 97.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA-directed RNA polymerase, subunit E' / Polymerase


Mass: 21893.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: Rpo7, TK1699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIY4
#2: Protein DNA-directed RNA polymerase, subunit F / Polymerase


Mass: 14519.659 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: Rpo4, TK0901 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JI52
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M NaAcetate and 30 % glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 0.9714 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 12, 2009
RadiationMonochromator: na / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9714 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 13248 / Num. obs: 12575 / % possible obs: 86.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
Crystalcleardata collection
PHENIXmodel building
PHENIX(phenix.refine: dev_1626)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 2.312→25.794 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 673 5.08 %5%
Rwork0.1928 ---
obs0.1963 12575 86.63 %-
all-84450 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.312→25.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2527 0 0 137 2664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082573
X-RAY DIFFRACTIONf_angle_d1.2123462
X-RAY DIFFRACTIONf_dihedral_angle_d17.2641019
X-RAY DIFFRACTIONf_chiral_restr0.044376
X-RAY DIFFRACTIONf_plane_restr0.006449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3115-2.48990.34431350.24852391X-RAY DIFFRACTION84
2.4899-2.74020.29091330.22042837X-RAY DIFFRACTION99
2.7402-3.13610.30481690.21232858X-RAY DIFFRACTION100
3.1361-3.94890.3045910.211655X-RAY DIFFRACTION90
3.9489-25.79580.18861450.15262833X-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)
10.4785-0.0474-0.49330.13630.52051.10190.0420.0754-0.0168-0.0752-0-0.0533-0.3278-0.16760.01750.15730.0139-0.00580.11950.01170.0843-2.92097.2343-42.8383
2-0.0154-0.03890.34160.1088-0.22220.21020.0598-0.1146-0.09520.0294-0.10310.0320.18910.0963-00.19130.0055-0.0260.23390.03730.184310.1436-1.6345-9.7129
30.0312-0.17570.03170.1301-0.08470.22330.080.0840.0106-0.0672-0.1002-0.05990.09260.1163-0.0020.14620.00010.0020.2297-0.01630.20379.24275.4715-24.8502
40.0131-0.0196-0.0490.1479-0.10570.03750.0387-0.36610.19990.2061-0.05460.0948-0.2577-0.04630.00020.2093-0.10290.01250.3609-0.05220.20971.564910.0426-2.7188
50.1817-0.43250.03170.72370.41960.7341-0.06890.03310.0826-0.7709-0.1570.7448-0.2941-0.1132-0.03970.2776-0.0503-0.05940.15760.00190.1692-6.779210.8168-35.1162
60.37890.23510.33190.33460.03650.62250.24990.4104-0.1393-0.779-0.11630.17630.28030.5234-0.03970.4162-0.0038-0.16760.07810.00530.3092-9.8396-5.1268-42.1997
7-0.1423-0.4097-0.14021.224-0.56060.2804-0.1140.05110.02770.11180.1520.1478-0.0806-0.0780.00540.14090.022-0.00160.109-0.01330.1761-6.57917.0277-17.8647
80.05090.0106-0.10880.02080.03630.57450.3278-0.1145-0.2601-0.39290.36740.3304-0.44040.36660.00430.24630.00060.02160.40760.140.4631-17.891711.8984-12.4735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 93 )
2X-RAY DIFFRACTION2chain 'A' and (resid 94 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 164 )
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 186 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 26 )
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 38 )
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 116 )
8X-RAY DIFFRACTION8chain 'B' and (resid 117 through 122 )

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