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- PDB-3tj1: Crystal Structure of RNA Polymerase I Transcription Initiation Fa... -

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Basic information

Entry
Database: PDB / ID: 3tj1
TitleCrystal Structure of RNA Polymerase I Transcription Initiation Factor Rrn3
ComponentsRNA polymerase I-specific transcription initiation factor RRN3
KeywordsTRANSCRIPTION / HEAT repeat / Transcription Factor / Nucleus
Function / homologyRNA polymerase I specific transcription initiation factor RRN3 / RNA polymerase I specific transcription initiation factor RRN3 / RNA Polymerase I Transcription Initiation / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core binding / RNA polymerase I general transcription initiation factor binding / transcription initiation from RNA polymerase I promoter / rDNA binding / nucleolus / nucleus / RNA polymerase I-specific transcription initiation factor RRN3
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 2.85 Å resolution
AuthorsBlattner, C. / Jennebach, S. / Herzog, F. / Mayer, A. / Cheung, A.C.M. / Witte, G. / Lorenzen, K. / Hopfner, K.-P. / Heck, A.J.R. / Aebersold, R. / Cramer, P.
CitationJournal: Genes Dev. / Year: 2011
Title: Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth.
Authors: Blattner, C. / Jennebach, S. / Herzog, F. / Mayer, A. / Cheung, A.C. / Witte, G. / Lorenzen, K. / Hopfner, K.P. / Heck, A.J. / Aebersold, R. / Cramer, P.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 23, 2011 / Release: Sep 28, 2011
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 28, 2011Structure modelrepositoryInitial release
1.1Oct 5, 2011Structure modelDatabase references
1.2Oct 19, 2011Structure modelDatabase references
1.3Jan 24, 2018Structure modelData collection / Structure summaryaudit_author / diffrn_audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase I-specific transcription initiation factor RRN3
B: RNA polymerase I-specific transcription initiation factor RRN3


Theoretical massNumber of molelcules
Total (without water)149,6642
Polyers149,6642
Non-polymers00
Water1,856103
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)2730
ΔGint (kcal/M)-10
Surface area (Å2)41720
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)96.770, 101.770, 162.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide RNA polymerase I-specific transcription initiation factor RRN3


Mass: 74831.883 Da / Num. of mol.: 2
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Strain: ATCC 204508 / S288c / Gene: RRN3, YKL125W / Plasmid name: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P36070
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Formula: H2O / Water

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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: 2.67 / Density percent sol: 53.85 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 14% PEG 3350, 250 mM sodium-potassium-tartrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0086, 1.0094, 1.0129
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Collection date: Sep 22, 2008
RadiationMonochromator: Liquid nitrogen cooled channel-cut silicon monochromator Si(111)
Diffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
11.00861.0
21.00941.0
31.01291.0
ReflectionD resolution high: 2.85 Å / D resolution low: 50 Å / Number all: 38079 / Number obs: 38054 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Percent possible obs: 99.9
Reflection shellHighest resolution: 2.85 Å / Lowest resolution: 2.92 Å / Percent possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHARPphasing
BUSTER2.11.1refinement
XDSdata reduction
XSCALEdata scaling
RefineMethod to determine structure: MAD / Correlation coeff Fo to Fc: 0.9308 / Correlation coeff Fo to Fc free: 0.9165 / Overall SU R Cruickshank DPI: 0.701 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Displacement parametersB iso mean: 62.5 Å2 / Aniso B11: 7.8169 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -23.5086 Å2 / Aniso B23: 0 Å2 / Aniso B33: 15.6916 Å2
Least-squares processR factor R free: 0.2418 / R factor R work: 0.2082 / R factor obs: 0.2099 / Highest resolution: 2.85 Å / Lowest resolution: 48.55 Å / Number reflection R free: 1900 / Number reflection all: 38079 / Number reflection obs: 38054 / Percent reflection R free: 4.99 / Percent reflection obs: 99.96
Refine analyzeLuzzati coordinate error obs: 0.436 Å
Refine hist #LASTHighest resolution: 2.85 Å / Lowest resolution: 48.55 Å
Number of atoms included #LASTProtein: 7972 / Nucleic acid: 0 / Ligand: 0 / Solvent: 103 / Total: 8075
Refine LS restraints
Refine IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0108152HARMONIC2.00
X-RAY DIFFRACTIONt_angle_deg1.1311017HARMONIC2.00
X-RAY DIFFRACTIONt_dihedral_angle_d2891SINUSOIDAL2.00
X-RAY DIFFRACTIONt_trig_c_planes208HARMONIC2.00
X-RAY DIFFRACTIONt_gen_planes1145HARMONIC5.00
X-RAY DIFFRACTIONt_it8152HARMONIC20.00
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion20.59
X-RAY DIFFRACTIONt_chiral_improper_torsion1072SEMIHARMONIC5.00
X-RAY DIFFRACTIONt_ideal_dist_contact9979SEMIHARMONIC4.00
Refine LS shellHighest resolution: 2.85 Å / R factor R free: 0.2524 / R factor R work: 0.2416 / R factor all: 0.2421 / Lowest resolution: 2.93 Å / Number reflection R free: 136 / Number reflection R work: 2771 / Number reflection all: 2907 / Total number of bins used: 19 / Percent reflection R free: 4.68 / Percent reflection obs: 99.96
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.6201-0.23241.39130.2875-0.38203.1169-0.1462-0.2317-0.0014-0.03980.12790.1204-0.2250-0.65560.0183-0.16230.0723-0.00520.17870.0070-0.163128.934229.9838110.5500
20.71880.67011.57660.26810.82812.8058-0.08170.25250.0089-0.00640.1298-0.1003-0.07050.7183-0.0481-0.12920.03600.00220.2856-0.0314-0.141477.678830.4171132.5290
Refine TLS group

Beg auth seq ID: 46 / End auth seq ID: 617 / Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDEnd auth asym IDRefine TLS IDSelection details
1AA1{ A|* }
2BB2{ B|* }

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