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- PDB-3e2e: Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA -

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Basic information

Entry
Database: PDB / ID: 3e2e
TitleCrystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA
Components
  • DNA (28-MER)
  • DNA (31-MER)
  • DNA-directed RNA polymerasePolymerase
  • RNA (5'-R(*GP*GP*GP*AP*GP*UP*G)-3')
KeywordsTransferase/RNA/DNA / T7 RNA Polymerase / DNA-directed RNA Polymerase / Transcription / Nucleotidyltransferase / Transferase / Transferase-RNA-DNA COMPLEX
Function / homology
Function and homology information


DNA-templated viral transcription / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding
Similarity search - Function
T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / Helix Hairpins - #260 / Helix Hairpins - #280 / DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal ...T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / Helix Hairpins - #260 / Helix Hairpins - #280 / DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Helix Hairpins / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / T7 RNA polymerase
Similarity search - Component
Biological speciesBacteriophage T7 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsDurniak, K.J. / Bailey, S. / Steitz, T.A.
CitationJournal: Science / Year: 2008
Title: The structure of a transcribing t7 RNA polymerase in transition from initiation to elongation
Authors: Durniak, K.J. / Bailey, S. / Steitz, T.A.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_radiation_wavelength / diffrn_source ...diffrn_radiation_wavelength / diffrn_source / entity_src_gen / pdbx_entity_src_syn / software
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase
R: RNA (5'-R(*GP*GP*GP*AP*GP*UP*G)-3')
T: DNA (31-MER)
N: DNA (28-MER)


Theoretical massNumber of molelcules
Total (without water)122,3484
Polymers122,3484
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-25 kcal/mol
Surface area46260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.008, 81.008, 358.791
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein DNA-directed RNA polymerase / Polymerase


Mass: 99829.156 Da / Num. of mol.: 1 / Mutation: P266L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage T7 (virus) / Gene: 1 / Plasmid: pBH161 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00573, DNA-directed RNA polymerase
#2: RNA chain RNA (5'-R(*GP*GP*GP*AP*GP*UP*G)-3')


Mass: 2316.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (31-MER)


Mass: 10121.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template DNA / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (28-MER)


Mass: 10080.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Non-template DNA / Source: (synth.) synthetic construct (others)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 6000, MgCl2, Tris ph8.0 at 285K, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2PEG 600012
3MgCl211
4MgCl212
5Tris11
6Tris12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 27490 / % possible obs: 93.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.081
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-32.50.62149.4
3-3.124.10.485188.9
3.12-3.276.30.371199.7
3.27-3.4470.2451100
3.44-3.6570.1611100
3.65-3.9470.117199.9
3.94-4.3370.096199.9
4.33-4.9670.086199.9
4.96-6.246.90.0821100
6.24-506.80.052198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→37.8 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / Occupancy max: 1 / Occupancy min: 1 / SU B: 56.162 / SU ML: 0.47 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29162 1330 5.1 %RANDOM
Rwork0.24044 ---
obs0.24296 24767 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.918 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å20 Å2
2--0.82 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 3→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6589 1351 0 73 8013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0228248
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1812.15911435
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.935826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.43124.169307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.638151181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0481539
X-RAY DIFFRACTIONr_chiral_restr0.0970.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025770
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.23845
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.25469
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0851.54300
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.14326654
X-RAY DIFFRACTIONr_scbond_it0.10225035
X-RAY DIFFRACTIONr_scangle_it0.1652.54781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 84 -
Rwork0.346 1521 -
obs--83.59 %
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)
17.912-1.5743-1.85766.01291.4885.54140.2337-0.21330.25010.9909-0.420.18320.1068-0.6370.1863-0.0012-0.1299-0.0666-0.38870.1672-0.463331.1692-45.687815.4715
26.0164-0.2453.87032.0388-0.73613.58580.3086-0.19030.17540.4533-0.12450.1729-0.127-0.5907-0.1842-0.2459-0.05340.206-0.08820.0859-0.306412.1021-45.70344.6086
35.8361-0.3082.48412.4018-0.72893.60330.1374-0.04870.54110.2227-0.11540.4071-0.1854-0.4013-0.022-0.23210.03680.1642-0.33610.1185-0.276419.198-39.35551.055
44.12852.38-1.46763.0440.8228.13630.04020.0818-0.43950.3006-0.37290.01560.4890.09160.3327-0.41380.0421-0.1355-0.45650.0336-0.436840.659-45.8019-1.1125
53.2049-1.95771.87886.1152-2.73933.29320.1935-0.01260.770.3771-0.21530.3786-0.9063-0.41970.02180.1475-0.080.0225-0.0956-0.0202-0.20232.359-12.88224.0441
62.03510.2617-0.37182.00130.3233.23960.2892-0.09330.46750.5879-0.3719-0.644-0.67820.92040.0827-0.2426-0.2741-0.2098-0.09940.1853-0.133355.5438-22.09923.4502
73.2280.8660.43792.83741.61246.703-0.00480.0574-0.14070.1288-0.4271-0.99970.22440.90110.4319-0.5817-0.0122-0.1774-0.02940.2114-0.163259.1123-35.6266-4.9114
80.2964-0.76410.24383.87960.29390.6459-0.17560.54860.2397-0.3344-0.0642-0.0987-0.39290.07970.2398-0.28410.06610.12360.23220.2616-0.009943.0131-18.7576-24.1263
98.33362.97186.04821.06062.19025.82460.08981.33770.3723-0.40220.11870.1461-0.0338-0.5042-0.2084-0.5610.17990.0990.16210.128-0.207639.2037-35.0652-24.0285
1023.57246.4792-5.19043.0442-3.5814.8166-0.1685-0.1097-0.09310.10690.45270.05970.4180.4417-0.2841-0.42760.1426-0.03010.072-0.10830.029113.5699-39.7744-15.7757
115.4783.83834.34984.98983.60885.94940.09810.7489-0.2663-0.13050.1511-0.8246-0.04590.4242-0.2492-0.53410.11590.1750.30040.1223-0.082655.7107-37.8451-26.4074
122.92132.19690.3522.1666-0.63241.6072-0.37670.39820.3819-0.67010.26620.1277-0.2347-0.03040.1105-0.1220.19780.06090.25540.09920.502516.2082-35.9936-21.7069
133.34172.9234-1.14523.2492-0.3722.1089-0.56330.62190.3623-0.46590.715-0.455-0.46320.28-0.1518-0.02660.0742-0.20730.42410.12840.321113.2553-32.2404-24.8672
143.2647-0.9348-6.324754.44154.01912.3429-0.67960.80010.8674-0.0087-0.0980.777-1.1217-0.46380.77760.04320.03050.0846-0.02180.2046-0.467234.2974-22.7839-8.4072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 5615 - 62
2X-RAY DIFFRACTION2AA73 - 16379 - 169
3X-RAY DIFFRACTION3AA178 - 254184 - 260
4X-RAY DIFFRACTION4AA264 - 324270 - 330
5X-RAY DIFFRACTION5AA325 - 410331 - 416
6X-RAY DIFFRACTION6AA411 - 552417 - 558
7X-RAY DIFFRACTION7AA784 - 836790 - 842
8X-RAY DIFFRACTION8AA553 - 738559 - 744
9X-RAY DIFFRACTION9AA769 - 783775 - 789
10X-RAY DIFFRACTION10AA739 - 768745 - 774
11X-RAY DIFFRACTION11AA837 - 883843 - 889
12X-RAY DIFFRACTION12TC1 - 161 - 16
13X-RAY DIFFRACTION12TC1919
14X-RAY DIFFRACTION12TC20 - 3320 - 33
15X-RAY DIFFRACTION13ND101 - 1131 - 13
16X-RAY DIFFRACTION13ND119 - 13319 - 33
17X-RAY DIFFRACTION14RB1 - 71 - 7

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