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- PDB-1ynn: Taq RNA polymerase-rifampicin complex -

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Basic information

Entry
Database: PDB / ID: 1ynn
TitleTaq RNA polymerase-rifampicin complex
Components(DNA-directed RNA polymerase ...Polymerase) x 4
KeywordsTRANSFERASE / RNA polymerase / RIFAMPICIN
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
RIFAMPICIN / 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: 3.3 Å
AuthorsCampbell, E.A. / Pavlova, O. / Zenkin, N. / Leon, F. / Irschik, H. / Jansen, R. / Severinov, K. / Darst, S.A.
Citation
Journal: 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.
#1: Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural mechanism for rifampicin inhibition of bacterial RNA polymerase
Authors: Campbell, E.A. / Korzheva, N. / Mustaev, A. / Murakami, K. / Goldfarb, A. / 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 / Refinement description / 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)549,5639
Polymers548,6096
Non-polymers9543
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41730 Å2
ΔGint-241 kcal/mol
Surface area133970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.760, 200.760, 292.938
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-RFP / RIFAMPICIN / Rifampicin


Mass: 822.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58N4O12 / Comment: antibiotic*YM
#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: 3.93 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, magnesium sulfate, ammonium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03321 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Sep 1, 1999
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 87596 / Num. obs: 75420 / % possible obs: 86.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.3→3.42 Å / % possible all: 71.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.781 / SU B: 39.948 / SU ML: 0.624 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.679 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.33051 3874 5.1 %RANDOM
Rwork0.27138 ---
obs0.27441 72697 84.94 %-
all-85586 --
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: 48.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24307 0 61 0 24368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02124824
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.331.97933662
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75253145
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_restr0.0910.23821
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218894
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.212366
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2835
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5971.515688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.112225197
X-RAY DIFFRACTIONr_scbond_it1.01539136
X-RAY DIFFRACTIONr_scangle_it1.9124.58465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.421 202
Rwork0.366 4407
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)
10.51230.0964-0.15210.49110.09441.11160.0656-0.0028-0.18230.1696-0.0880.07510.0159-0.06360.02240.2546-0.09080.08770.1273-0.14740.172339.46784.45752.708
2-0.5090.1562-1.7721.1723-0.2094.1419-0.11580.1998-0.0596-0.4330.2044-0.3459-0.1271-0.1755-0.08860.38560.000100.385700.385751.454104.26-3.577
32.57373.792-3.94884.4651.38716.48670.04880.33470.2880.01780.2098-0.3694-0.1817-0.1636-0.25860.3857000.385600.385767.531127.90816.347
40.7928-4.2818-2.31794.08581.16711.65280.0611-0.14580.0613-0.3283-0.5161-0.03940.360.4860.45490.3856-0.000100.3856-0.00010.385750.11162.7779.768
55.05021.8783-2.50310.74430.40532.2723-0.19110.3565-0.0972-0.57280.2962-0.17630.15480.083-0.10510.3857000.385700.385790.84776.64325.065
694.281-14.77954.165397.6752-8.8398139.8808-0.7065-0.84851.56020.42110.4430.3224-0.9824-2.76720.26350.3866-0.000500.38620.00010.3856119.867105.059-9.493
794.84682.58057.246974.9577-7.762172.60430.17192.13551.2132-1.0685-0.36642.6367-0.7785-0.77190.19450.386-0.00070.00120.38540.00010.3861131.296.491-26.325
824.29016.88210.875720.68426.500936.56280.27020.165-0.10430.4587-0.12690.586-0.6412-0.5357-0.14340.38570.0001-0.00020.38580.00010.3858151.102113.59-43.414
932.9996.5423-13.253127.255612.6153.48570.7509-1.17921.2427-0.2914-0.94290.6792-1.20140.20570.1920.3860.0001-0.00020.3859-0.00010.3859132.52992.931.218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 235
2X-RAY DIFFRACTION1B4 - 228
3X-RAY DIFFRACTION1C1 - 21
4X-RAY DIFFRACTION1C131 - 141
5X-RAY DIFFRACTION1C325 - 335
6X-RAY DIFFRACTION1C393 - 704
7X-RAY DIFFRACTION1C829 - 1057
8X-RAY DIFFRACTION1D620 - 1240
9X-RAY DIFFRACTION1J1253 - 1435
10X-RAY DIFFRACTION1J1460 - 1501
11X-RAY DIFFRACTION1K1 - 95
12X-RAY DIFFRACTION1D1525
13X-RAY DIFFRACTION1C1120
14X-RAY DIFFRACTION2C22 - 130
15X-RAY DIFFRACTION2C336 - 392
16X-RAY DIFFRACTION3C142 - 324
17X-RAY DIFFRACTION4C705 - 828
18X-RAY DIFFRACTION5C1058 - 1114
19X-RAY DIFFRACTION5D3 - 162
20X-RAY DIFFRACTION5D451 - 619
21X-RAY DIFFRACTION5J1436 - 1459
22X-RAY DIFFRACTION5D1526
23X-RAY DIFFRACTION6D164 - 208
24X-RAY DIFFRACTION6D389 - 397
25X-RAY DIFFRACTION7D209 - 216
26X-RAY DIFFRACTION7D340 - 388
27X-RAY DIFFRACTION8D217 - 339
28X-RAY DIFFRACTION9D398 - 450

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