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- PDB-1ynj: Taq RNA polymerase-Sorangicin complex -

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Basic information

Entry
Database: PDB / ID: 1ynj
TitleTaq RNA polymerase-Sorangicin complex
Components(DNA-directed RNA polymerase ...Polymerase) x 4
KeywordsTRANSFERASE
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
PTS-regulatory domain, PRD - #20 / PTS-regulatory domain, PRD / DNA polymerase; domain 1 - #390 / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / : ...PTS-regulatory domain, PRD - #20 / PTS-regulatory domain, PRD / DNA polymerase; domain 1 - #390 / Rna Polymerase Beta Subunit; Chain: C,domain 2 / Rna Polymerase Beta Subunit; Chain: C,domain 2 - #10 / Rna Polymerase Beta Subunit; Chain: C, domain 4 / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / : / DNA-directed RNA polymerase subunit beta', hybrid domain / Enzyme I; Chain A, domain 2 / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Gyrase A; domain 2 / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / Beta Complex / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SORANGICIN A / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.2 Å
AuthorsCampbell, E.A. / Pavlova, O. / Zenkin, N. / Leon, F. / Irschik, H. / Jansen, R. / Severinov, K. / Darst, S.A.
CitationJournal: Embo J. / Year: 2005
Title: Structural, functional, and genetic analysis of sorangicin inhibition of bacterial RNA polymerase
Authors: Campbell, E.A. / Pavlova, O. / Zenkin, N. / Leon, F. / Irschik, H. / Jansen, R. / Severinov, K. / Darst, S.A.
History
DepositionJan 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 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 / struct_conn / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase alpha chain
B: DNA-directed RNA polymerase alpha chain
C: DNA-directed RNA polymerase beta chain
D: DNA-directed RNA polymerase beta' chain
J: DNA-directed RNA polymerase beta' chain
K: DNA-directed RNA polymerase omega chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)549,5479
Polymers548,6096
Non-polymers9383
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41810 Å2
ΔGint-243 kcal/mol
Surface area131540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.190, 199.190, 289.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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DNA-directed RNA polymerase ... , 4 types, 6 molecules ABCDJK

#1: Protein DNA-directed RNA polymerase alpha chain / RNAP alpha subunit / Transcriptase alpha chain / RNA polymerase alpha subunit


Mass: 34830.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU8, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase beta chain / RNAP beta subunit / Transcriptase beta chain / RNA polymerase beta subunit


Mass: 124930.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase beta' chain / RNAP beta' subunit / Transcriptase beta' chain / RNA polymerase beta' subunit


Mass: 171187.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU6, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase omega chain / RNAP omega subunit / Transcriptase omega chain / RNA polymerase omega subunit


Mass: 11642.423 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9EVV4, DNA-directed RNA polymerase

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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-SRN / SORANGICIN A


Mass: 807.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H66O11
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.82 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, ammonium formate, magnesium formate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. all: 94908 / Num. obs: 93484 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.2→3.31 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.2→40 Å / Cor.coef. Fo:Fc: 0.843 / Cor.coef. Fo:Fc free: 0.778 / SU B: 30.294 / SU ML: 0.515 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.618 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.34614 4504 5 %RANDOM
Rwork0.28119 ---
obs0.28442 84957 93.09 %-
all-91263 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.761 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 3.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24309 0 60 0 24369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02124825
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.97933654
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21753145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.23827
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218877
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2620.213272
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.21002
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7331.515688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.359225197
X-RAY DIFFRACTIONr_scbond_it1.25639137
X-RAY DIFFRACTIONr_scangle_it2.3034.58457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.412 316
Rwork0.368 6086
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.20280.0432-0.28090.2995-0.05280.90860.0483-0.0297-0.03840.1919-0.05490.1036-0.1952-0.00560.00660.2967-0.17580.06280.135-0.10860.178239.46784.45752.708
2-0.49210.9694-2.40751.5815-0.57764.1007-0.00050.4705-0.14830.05010.1062-0.1488-0.3616-0.4974-0.10570.3102000.310100.310251.454104.26-3.577
3-0.75913.0439-1.5814.23330.46510.96130.04340.24660.21910.3063-0.1057-0.26120.2744-0.25140.06240.3102000.310200.310267.531127.90816.347
40.5232-2.3237-0.98340.36312.777-0.44060.2614-0.0657-0.1020.2638-0.29940.11160.32380.20550.0380.3101-0.00010.00020.3102-0.00010.310150.11162.7779.768
51.87581.1582-1.2281-0.97260.48761.24830.0242-0.1475-0.0531-0.05220.013-0.1529-0.19690.0796-0.03720.3102000.310200.310290.84776.64325.065
662.6625-15.622-12.232348.1566-37.151585.5005-0.70320.0397-0.4268-0.61540.4051.1399-2.6303-2.70990.29820.3104-0.00080.00040.31030.00010.3104119.867105.059-9.493
770.958312.6586-9.890442.5963-16.950754.39310.16872.5514-1.2824-0.2923-0.03891.6541.3103-0.6131-0.12990.310100.00080.31010.00080.3104131.296.491-26.325
814.38053.02979.82276.9095-0.377622.2344-0.5307-0.09660.25140.18650.58070.3071-0.82170.3673-0.050.3101-0.00010.00010.31010.00010.3103151.102113.59-43.414
916.89485.5259-7.4119.33061.762837.49220.73-0.60420.94070.9881-0.7442-1.2412-1.50180.18880.01430.31020.00020.00020.3105-0.00010.31132.52992.931.218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 2356 - 235
2X-RAY DIFFRACTION1BB4 - 2284 - 228
3X-RAY DIFFRACTION1CC1 - 211 - 21
4X-RAY DIFFRACTION1CC131 - 141131 - 141
5X-RAY DIFFRACTION1CC325 - 335325 - 335
6X-RAY DIFFRACTION1CC393 - 704393 - 704
7X-RAY DIFFRACTION1CC829 - 1057829 - 1057
8X-RAY DIFFRACTION1DD620 - 1240620 - 1240
9X-RAY DIFFRACTION1JE1253 - 14351253 - 1435
10X-RAY DIFFRACTION1JE1460 - 15011460 - 1501
11X-RAY DIFFRACTION1KF1 - 951 - 95
12X-RAY DIFFRACTION1DH15251
13X-RAY DIFFRACTION1CG11201
14X-RAY DIFFRACTION2CC22 - 13022 - 130
15X-RAY DIFFRACTION2CC336 - 392336 - 392
16X-RAY DIFFRACTION3CC142 - 324142 - 324
17X-RAY DIFFRACTION4CC705 - 828705 - 828
18X-RAY DIFFRACTION5CC1058 - 11141058 - 1114
19X-RAY DIFFRACTION5DD3 - 1623 - 162
20X-RAY DIFFRACTION5DD451 - 619451 - 619
21X-RAY DIFFRACTION5JE1436 - 14591436 - 1459
22X-RAY DIFFRACTION5DI15261
23X-RAY DIFFRACTION6DD163 - 208163 - 208
24X-RAY DIFFRACTION6DD389 - 397389 - 397
25X-RAY DIFFRACTION7DD209 - 216209 - 216
26X-RAY DIFFRACTION7DD340 - 388340 - 388
27X-RAY DIFFRACTION8DD217 - 339217 - 339
28X-RAY DIFFRACTION9DD398 - 450398 - 450

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