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- PDB-5eev: RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 3.88 MGy -

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Basic information

Entry
Database: PDB / ID: 5eev
TitleRADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 3.88 MGy
Components
  • (GAGUU)10GAG 53-NUCLEOTIDE RNA
  • Transcription attenuation protein MtrB
KeywordsRNA BINDING PROTEIN / protein-RNA complex / radiation damage / RNA-binding protein
Function / homology
Function and homology information


DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding
Similarity search - Function
TRAP-like / Transcription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein domain / Tryptophan RNA-binding attenuator protein / Tryptophan RNA-binding attenuator protein-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRYPTOPHAN / RNA / RNA (> 10) / Transcription attenuation protein MtrB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBury, C.S. / McGeehan, J.E. / Garman, E.F. / Shevtsov, M.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2016
Title: RNA protects a nucleoprotein complex against radiation damage.
Authors: Bury, C.S. / McGeehan, J.E. / Antson, A.A. / Carmichael, I. / Gerstel, M. / Shevtsov, M.B. / Garman, E.F.
#1: Journal: Acta Crystallogr D Biol Crystallogr. / Year: 2002
Title: Specificity of TRAP-RNA interactions: crystal structures of two complexes with different RNA sequences
Authors: Hopcroft, N.H. / Wendt, A.L. / Gollnick, P. / Antson, A.A.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription attenuation protein MtrB
B: Transcription attenuation protein MtrB
C: Transcription attenuation protein MtrB
D: Transcription attenuation protein MtrB
E: Transcription attenuation protein MtrB
F: Transcription attenuation protein MtrB
G: Transcription attenuation protein MtrB
H: Transcription attenuation protein MtrB
I: Transcription attenuation protein MtrB
J: Transcription attenuation protein MtrB
K: Transcription attenuation protein MtrB
L: Transcription attenuation protein MtrB
M: Transcription attenuation protein MtrB
N: Transcription attenuation protein MtrB
O: Transcription attenuation protein MtrB
P: Transcription attenuation protein MtrB
Q: Transcription attenuation protein MtrB
R: Transcription attenuation protein MtrB
S: Transcription attenuation protein MtrB
T: Transcription attenuation protein MtrB
U: Transcription attenuation protein MtrB
V: Transcription attenuation protein MtrB
W: (GAGUU)10GAG 53-NUCLEOTIDE RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,06245
Polymers199,56923
Non-polymers4,49322
Water13,385743
1
A: Transcription attenuation protein MtrB
B: Transcription attenuation protein MtrB
C: Transcription attenuation protein MtrB
D: Transcription attenuation protein MtrB
E: Transcription attenuation protein MtrB
F: Transcription attenuation protein MtrB
G: Transcription attenuation protein MtrB
H: Transcription attenuation protein MtrB
I: Transcription attenuation protein MtrB
J: Transcription attenuation protein MtrB
K: Transcription attenuation protein MtrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,07822
Polymers90,83111
Non-polymers2,24611
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25490 Å2
ΔGint-104 kcal/mol
Surface area27560 Å2
MethodPISA
2
L: Transcription attenuation protein MtrB
M: Transcription attenuation protein MtrB
N: Transcription attenuation protein MtrB
O: Transcription attenuation protein MtrB
P: Transcription attenuation protein MtrB
Q: Transcription attenuation protein MtrB
R: Transcription attenuation protein MtrB
S: Transcription attenuation protein MtrB
T: Transcription attenuation protein MtrB
U: Transcription attenuation protein MtrB
V: Transcription attenuation protein MtrB
W: (GAGUU)10GAG 53-NUCLEOTIDE RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,98423
Polymers108,73812
Non-polymers2,24611
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37450 Å2
ΔGint-141 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.000, 110.980, 137.930
Angle α, β, γ (deg.)90.000, 117.410, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ...
Transcription attenuation protein MtrB / Trp RNA-binding attenuation protein / TRAP / Tryptophan RNA-binding attenuator protein


Mass: 8257.377 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mtrB / Plasmid: PTZSTMTRB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG62052/PGP1-2 / References: UniProt: Q9X6J6
#2: RNA chain (GAGUU)10GAG 53-NUCLEOTIDE RNA


Mass: 17906.479 Da / Num. of mol.: 1 / Fragment: (GAGUU)10GAG 53-NUCLEOTIDE RNA / Source method: obtained synthetically / Details: SYNTHETIC RNA. IN-VITRO TRANSCRIPTION / Source: (synth.) synthetic construct (others)
#3: Chemical...
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 22 / Fragment: Trp ligands / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Potassium phosphate,L-tryptophan,potassium glutamate,triethanolamine,MgCl2,monomethyl ether PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.98→62.59 Å / Num. obs: 130202 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.057 / Net I/σ(I): 9.4 / Num. measured all: 471462 / Scaling rejects: 22
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.98-2.013.40.9461.42163463590.7720.58898.2
10.84-62.593.50.02226.528478050.9990.01495.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.3.11data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gtf

1gtf


Resolution: 1.98→58.554 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 6547 5.03 %5% random selection
Rwork0.2092 123530 --
obs0.211 130077 99.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.65 Å2 / Biso mean: 34.4697 Å2 / Biso min: 17.11 Å2
Refinement stepCycle: final / Resolution: 1.98→58.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11789 968 330 743 13830
Biso mean--27.88 39.71 -
Num. residues----1565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02413392
X-RAY DIFFRACTIONf_angle_d2.27618220
X-RAY DIFFRACTIONf_chiral_restr0.1692108
X-RAY DIFFRACTIONf_plane_restr0.0122156
X-RAY DIFFRACTIONf_dihedral_angle_d15.6494912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.979-2.00150.38082190.3474019423898
2.0015-2.0250.34032260.33414062428898
2.025-2.04970.38722310.32954048427999
2.0497-2.07570.32412080.32324135434399
2.0757-2.1030.35582170.29974089430699
2.103-2.13180.31322210.29014064428598
2.1318-2.16230.31032340.2924023425799
2.1623-2.19450.28392160.27834123433999
2.1945-2.22880.29931940.26464146434099
2.2288-2.26540.29532300.26454083431399
2.2654-2.30440.26482150.25144082429799
2.3044-2.34630.29711960.24984130432699
2.3463-2.39150.33272330.24624064429799
2.3915-2.44030.272320.22944094432699
2.4403-2.49340.25722130.22654168438199
2.4934-2.55140.2941980.22714114431299
2.5514-2.61520.29362220.23434098432099
2.6152-2.68590.26362420.22774112435499
2.6859-2.76490.3052050.226741474352100
2.7649-2.85410.26332000.221641654365100
2.8541-2.95610.27472140.230841664380100
2.9561-3.07450.24492080.20841804388100
3.0745-3.21440.25052430.199141394382100
3.2144-3.38390.23752100.184541184328100
3.3839-3.59590.2182200.175141584378100
3.5959-3.87340.2012000.172741724372100
3.8734-4.26310.18622320.16141564388100
4.2631-4.87980.17142410.14614121436299
4.8798-6.14690.18532120.16644144435698
6.1469-58.57980.23042150.20874210442598

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