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- PDB-5eeu: RADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 1.31 MGy -

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Basic information

Entry
Database: PDB / ID: 5eeu
TitleRADIATION DAMAGE TO THE TRAP-RNA COMPLEX: DOSE (DWD) 1.31 MGy
Components
  • (GAGUU)10GAG 53-NUCLEOTIDE RNA
  • Transcription attenuation protein MtrB
KeywordsRNA BINDING PROTEIN / protein-RNA complex / radiation damage
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 / 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 area25520 Å2
ΔGint-104 kcal/mol
Surface area27520 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 area37460 Å2
ΔGint-140 kcal/mol
Surface area29840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.900, 110.890, 137.810
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: 2.4 Å3/Da / Density % sol: 48.79 %
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→62.54 Å / Num. obs: 129942 / % possible obs: 99.3 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.058 / Net I/σ(I): 9.6 / Num. measured all: 473080 / Scaling rejects: 36
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.5 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.98-2.010.8531.52182263160.8240.52998.2
10.84-62.540.02325.627978000.9990.01494.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
Aimless0.2.8data scaling
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gtf

1gtf


Resolution: 1.98→122.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 10.664 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 6535 5 %RANDOM
Rwork0.1897 ---
obs0.1918 123391 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.1 Å2 / Biso mean: 36.99 Å2 / Biso min: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å20.48 Å2
2--0.32 Å2-0 Å2
3----1.49 Å2
Refinement stepCycle: final / Resolution: 1.98→122.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11789 968 330 743 13830
Biso mean--28.3 40.9 -
Num. residues----1565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.01813392
X-RAY DIFFRACTIONr_angle_refined_deg2.271.86318220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.65951505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44223.639588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.723152192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9121588
X-RAY DIFFRACTIONr_chiral_restr0.1670.22064
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.029614
X-RAY DIFFRACTIONr_mcbond_it1.2651.6826134
X-RAY DIFFRACTIONr_mcangle_it1.9282.5067592
X-RAY DIFFRACTIONr_scbond_it2.0821.9177256
LS refinement shellResolution: 1.979→2.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 492 -
Rwork0.298 8959 -
all-9451 -
obs--98.24 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1834-0.57080.85151.3455-0.16024.4278-0.06820.0679-0.18120.04520.0502-0.00070.3794-0.07410.0180.236-0.03480.1590.0202-0.04370.2084-17.3347-29.956213.029
20.6678-0.17350.15392.6171-1.36554.4913-0.03750.0513-0.1097-0.0722-0.0430.07180.2763-0.27380.08050.189-0.08680.10260.0728-0.09570.1622-30.6186-24.24928.3359
31.08080.5131-0.82372.5628-1.15714.7121-0.00810.1404-0.1-0.1485-0.0160.13190.0902-0.39950.02410.1474-0.04570.04260.1625-0.11690.1257-38.7338-11.77925.5827
41.94931.2713-0.97582.3774-1.2053.9216-0.0050.17850.0363-0.1423-0.03680.1462-0.1288-0.46120.04180.15950.04160.00410.1765-0.07290.0752-39.60213.53725.4767
53.2790.8075-0.89831.6224-0.38843.23830.00910.1640.0731-0.0952-0.02520.0414-0.2892-0.24990.01610.19510.08390.01960.06970.00580.0578-32.18116.5298.0791
63.9677-0.2431-1.6191.6133-0.0743.13520.06880.08930.1977-0.0145-0.0354-0.035-0.41810.0679-0.03340.23760.00570.03620.02490.02030.0806-19.403223.618612.9321
73.6056-1.0695-1.43221.64230.43023.07220.15750.05410.2159-0.0564-0.1122-0.1421-0.35820.2314-0.04530.2145-0.07080.07550.05590.0110.1151-5.196721.96717.933
81.7615-0.9909-1.9013.08991.10073.53330.1125-0.16440.0455-0.0424-0.0612-0.2845-0.18160.4161-0.05120.1084-0.09140.08610.1580.00010.15486.077912.398921.809
91.4171-0.2278-1.01412.67521.76943.9973-0.0122-0.1836-0.0791-0.04220.0061-0.20860.06330.43590.0060.0597-0.00910.08230.21780.03020.18610.6993-2.049323.2562
101.36350.42420.71112.21521.90613.7151-0.1356-0.176-0.1595-0.060.0902-0.11680.21670.38160.04540.11290.07320.13470.16840.05580.20327.175-16.725121.6587
111.5047-0.12630.83810.99740.86335.0027-0.1513-0.017-0.15520.05250.0538-0.13890.44150.14070.09750.20930.05350.14780.04540.01630.2257-3.2463-27.140717.9689
121.31250.7723-0.40851.47811.02854.4107-0.0585-0.1201-0.12690.01450.0381-0.1640.26370.41290.02030.09610.08550.06830.20730.07160.1842-1.8071-10.793254.3145
131.15470.2964-1.22372.26141.31823.3627-0.0164-0.1867-0.01930.0085-0.0022-0.18660.00650.42970.01860.0536-0.01270.03220.21320.0510.1396-1.8754.219754.3055
141.4654-1.0522-1.52662.37730.16263.61340.0668-0.06830.10550.005-0.059-0.1706-0.17080.3426-0.00790.0981-0.08140.03380.1104-0.00180.1125-9.662316.858951.5345
152.8946-1.0577-1.14581.0486-0.37033.90920.03140.03080.1697-0.0186-0.0148-0.0282-0.26930.1674-0.01650.1589-0.0280.03710.02740.00050.0749-22.621123.087446.9167
163.4279-0.1249-1.41290.48160.16143.67940.01650.16620.137-0.08480.03630.1102-0.2614-0.138-0.05290.15410.04030.02220.06670.02350.0693-36.695120.917441.8654
173.18321.1922-1.12131.1098-0.13033.69690.00540.17690.0547-0.13940.01240.1713-0.2241-0.3214-0.01780.10410.05510.00770.1732-0.02040.0745-47.397510.993937.9557
181.73171.0335-1.12392.8852-0.84383.8273-0.01260.1828-0.0883-0.12210.00040.18730.0178-0.4180.01230.0776-0.05240.03050.2224-0.09460.0985-51.2904-3.524336.5116
191.03150.1731-0.84892.6889-1.27283.8116-0.01450.1475-0.185-0.0813-0.01670.10010.239-0.37350.03120.1594-0.11510.09950.1701-0.11650.155-47.1647-17.942537.9426
201.1296-0.5494-0.14131.636-1.27924.1877-0.01290.111-0.1534-0.0118-0.02460.0180.3839-0.15580.03750.2391-0.08290.14950.0774-0.0690.2039-36.3831-27.741341.7812
211.3352-0.19020.35581.3248-0.3724.6029-0.09880.0827-0.15270.07190.0789-0.050.38130.03760.01990.25440.02570.15960.04590.01110.2242-22.3376-29.819146.8394
222.14160.41410.29421.32320.56614.5185-0.1317-0.0541-0.1850.05990.0098-0.17170.4960.21710.12190.21240.10570.12120.09550.06460.222-9.4254-23.624251.51
231.35070.09390.24071.60180.13420.7851-0.06860.0609-0.0719-0.0596-0.0218-0.02020.06640.01480.09040.2943-0.01660.13990.2740.00060.0738-24-3.380539.9435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 81
2X-RAY DIFFRACTION2B7 - 81
3X-RAY DIFFRACTION3C6 - 81
4X-RAY DIFFRACTION4D7 - 81
5X-RAY DIFFRACTION5E7 - 81
6X-RAY DIFFRACTION6F7 - 81
7X-RAY DIFFRACTION7G7 - 81
8X-RAY DIFFRACTION8H7 - 81
9X-RAY DIFFRACTION9I7 - 81
10X-RAY DIFFRACTION10J7 - 81
11X-RAY DIFFRACTION11K7 - 81
12X-RAY DIFFRACTION12L5 - 81
13X-RAY DIFFRACTION13M5 - 81
14X-RAY DIFFRACTION14N5 - 81
15X-RAY DIFFRACTION15O5 - 81
16X-RAY DIFFRACTION16P5 - 81
17X-RAY DIFFRACTION17Q5 - 81
18X-RAY DIFFRACTION18R5 - 81
19X-RAY DIFFRACTION19S5 - 81
20X-RAY DIFFRACTION20T5 - 81
21X-RAY DIFFRACTION21U5 - 81
22X-RAY DIFFRACTION22V5 - 81
23X-RAY DIFFRACTION23W101 - 154

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