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- PDB-3k4g: Crystal structure of E. coli RNA polymerase alpha subunit C-termi... -

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Basic information

Entry
Database: PDB / ID: 3k4g
TitleCrystal structure of E. coli RNA polymerase alpha subunit C-terminal domain
ComponentsDNA-directed RNA polymerase subunit alphaPolymerase
KeywordsTRANSFERASE / BACTERIAL TRANSCRIPTION REGULATION / DNA-directed RNA polymerase / Nucleotidyltransferase / Transcription
Function / homology
Function and homology information


submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination ...submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / DNA-templated transcription initiation / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / protein dimerization activity / DNA binding / membrane / cytosol / cytoplasm
Similarity search - Function
RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / 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, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / 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 / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsLara-Gonzalez, S. / Birktoft, J. / Lawson, C.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structure of the Escherichia coli RNA polymerase alpha subunit C-terminal domain.
Authors: Lara-Gonzalez, S. / Birktoft, J.J. / Lawson, C.L.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit alpha
D: DNA-directed RNA polymerase subunit alpha
E: DNA-directed RNA polymerase subunit alpha
F: DNA-directed RNA polymerase subunit alpha
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,39112
Polymers78,2998
Non-polymers924
Water5,711317
1
A: DNA-directed RNA polymerase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8102
Polymers9,7871
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA-directed RNA polymerase subunit alpha


Theoretical massNumber of molelcules
Total (without water)9,7871
Polymers9,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA-directed RNA polymerase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8102
Polymers9,7871
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA-directed RNA polymerase subunit alpha


Theoretical massNumber of molelcules
Total (without water)9,7871
Polymers9,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: DNA-directed RNA polymerase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8102
Polymers9,7871
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: DNA-directed RNA polymerase subunit alpha


Theoretical massNumber of molelcules
Total (without water)9,7871
Polymers9,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: DNA-directed RNA polymerase subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8102
Polymers9,7871
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: DNA-directed RNA polymerase subunit alpha


Theoretical massNumber of molelcules
Total (without water)9,7871
Polymers9,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.342, 67.612, 116.553
Angle α, β, γ (deg.)90.000, 90.120, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and peptide backbone and (resseq 246:329 )A0
211chain B and peptide backbone and (resseq 246:328 )B0
311chain C and peptide backbone and (resseq 246:329 )C0
411chain D and peptide backbone and (resseq 246:328 )D0
511chain E and peptide backbone and (resseq 246:328 )E0
611chain F and peptide backbone and (resseq 246:329 )F0
711chain G and peptide backbone and (resseq 246:329 )G0
811chain H and peptide backbone and (resseq 246:328 )H0

NCS oper:
IDCodeMatrixVector
1given(-0.999695, -0.024045, 0.005662), (0.02459, -0.946749, 0.321032), (-0.002359, 0.321073, 0.947051)-25.8389, -14.9168, 2.45058
2given(0.999838, -0.009169, 0.015485), (-0.009145, -0.999957, -0.001595), (0.015499, 0.001453, -0.999879)-1.00297, -30.2293, -87.402397
3given(-0.999777, 0.018239, -0.010598), (0.020609, 0.951769, -0.306121), (0.004503, -0.306272, -0.951934)-24.486, -13.918, -89.968697
4given(0.999753, 0.022187, 0.000981), (-0.021352, 0.948133, 0.317157), (0.006107, -0.317099, 0.948373)-26.036501, 36.075298, -45.391602
5given(-0.999817, -0.014673, 0.012275), (0.014668, -0.999892, -0.000527), (0.012281, -0.000347, 0.999925)0.948905, -63.888199, -29.2673
6given(-0.999868, 0.002999, 0.015971), (0.002715, 0.999838, -0.017786), (-0.016021, -0.01774, -0.999714)0.268301, 33.334099, -59.1311
7given(0.999794, -0.019223, -0.006533), (-0.020296, -0.954222, -0.29841), (-0.000498, 0.298482, -0.954415)-26.7183, -65.684898, -43.167

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Components

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


Mass: 9787.382 Da / Num. of mol.: 8 / Fragment: Alpha C-terminal domain, residues 245-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b3295, JW3257, pez, phs, rpoA, sez / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M hepes, 1.4M sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 24, 2009
RadiationMonochromator: Si (111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.437
ReflectionResolution: 2.05→47.036 Å / Num. all: 50271 / Num. obs: 50235 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 12.9
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.1 / Num. measured all: 26693 / Num. unique all: 7266 / Rsym value: 0.544 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.02 Å
Translation2.5 Å47.02 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASER1.3.3phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LB2

1lb2


Resolution: 2.05→47.023 Å / Occupancy max: 1 / Occupancy min: 0.25 / Isotropic thermal model: Isotropic / σ(F): 1.38 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2000 3.98 %RANDOM
Rwork0.193 ---
obs0.194 50220 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.858 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 55.55 Å2 / Biso mean: 31.351 Å2 / Biso min: 16.26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→47.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5216 0 4 317 5537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035350
X-RAY DIFFRACTIONf_angle_d0.7757291
X-RAY DIFFRACTIONf_chiral_restr0.044866
X-RAY DIFFRACTIONf_plane_restr0.002926
X-RAY DIFFRACTIONf_dihedral_angle_d15.3052073
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A333X-RAY DIFFRACTIONPOSITIONAL0.172
12B333X-RAY DIFFRACTIONPOSITIONAL0.172
13C337X-RAY DIFFRACTIONPOSITIONAL0.116
14D333X-RAY DIFFRACTIONPOSITIONAL0.16
15E333X-RAY DIFFRACTIONPOSITIONAL0.166
16F335X-RAY DIFFRACTIONPOSITIONAL0.104
17G337X-RAY DIFFRACTIONPOSITIONAL0.111
18H331X-RAY DIFFRACTIONPOSITIONAL0.146
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 96 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2.05-2.1010.2491420.261337835203378
2.101-2.1580.2451430.242345435973454
2.158-2.2220.3081430.239339635393396
2.222-2.2930.2681380.232344635843446
2.293-2.3750.2981410.233339835393398
2.375-2.470.3031390.229343535743435
2.47-2.5830.2321430.228346336063463
2.583-2.7190.2821410.225345735983457
2.719-2.8890.2731410.214340835493408
2.889-3.1120.2521470.204343135783431
3.112-3.4240.2341440.184347136153471
3.424-3.9190.2551430.156343935823439
3.919-4.9340.1461450.133347036153470
4.934-29.1410.2271470.186355136983551

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