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- PDB-1c9s: CRYSTAL STRUCTURE OF A COMPLEX OF TRP RNA-BINDING ATTENUATION PRO... -

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Basic information

Entry
Database: PDB / ID: 1c9s
TitleCRYSTAL STRUCTURE OF A COMPLEX OF TRP RNA-BINDING ATTENUATION PROTEIN WITH A 53-BASE SINGLE STRANDED RNA CONTAINING ELEVEN GAG TRIPLETS SEPARATED BY AU DINUCLEOTIDES
Components
  • SINGLE STRANDED RNA (55-MER)
  • TRP RNA-BINDING ATTENUATION PROTEIN
KeywordsRNA BINDING PROTEIN/RNA / TRAP / PROTEIN-RNA COMPLEX / TRANSCRIPTION / SINGLE STRANDED RNA / RNA BINDING PROTEIN-RNA COMPLEX
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsAntson, A.A. / Dodson, E.J. / Dodson, G.G. / Greaves, R.B. / Chen, X.-P. / Gollnick, P.
CitationJournal: Nature / Year: 1999
Title: Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA.
Authors: Antson, A.A. / Dodson, E.J. / Dodson, G. / Greaves, R.B. / Chen, X. / Gollnick, P.
History
DepositionAug 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _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
W: SINGLE STRANDED RNA (55-MER)
A: TRP RNA-BINDING ATTENUATION PROTEIN
B: TRP RNA-BINDING ATTENUATION PROTEIN
C: TRP RNA-BINDING ATTENUATION PROTEIN
D: TRP RNA-BINDING ATTENUATION PROTEIN
E: TRP RNA-BINDING ATTENUATION PROTEIN
F: TRP RNA-BINDING ATTENUATION PROTEIN
G: TRP RNA-BINDING ATTENUATION PROTEIN
H: TRP RNA-BINDING ATTENUATION PROTEIN
I: TRP RNA-BINDING ATTENUATION PROTEIN
J: TRP RNA-BINDING ATTENUATION PROTEIN
K: TRP RNA-BINDING ATTENUATION PROTEIN
L: TRP RNA-BINDING ATTENUATION PROTEIN
M: TRP RNA-BINDING ATTENUATION PROTEIN
N: TRP RNA-BINDING ATTENUATION PROTEIN
O: TRP RNA-BINDING ATTENUATION PROTEIN
P: TRP RNA-BINDING ATTENUATION PROTEIN
Q: TRP RNA-BINDING ATTENUATION PROTEIN
R: TRP RNA-BINDING ATTENUATION PROTEIN
S: TRP RNA-BINDING ATTENUATION PROTEIN
T: TRP RNA-BINDING ATTENUATION PROTEIN
U: TRP RNA-BINDING ATTENUATION PROTEIN
V: TRP RNA-BINDING ATTENUATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,51946
Polymers199,82223
Non-polymers4,69723
Water22,7711264
1
A: TRP RNA-BINDING ATTENUATION PROTEIN
B: TRP RNA-BINDING ATTENUATION PROTEIN
C: TRP RNA-BINDING ATTENUATION PROTEIN
D: TRP RNA-BINDING ATTENUATION PROTEIN
E: TRP RNA-BINDING ATTENUATION PROTEIN
F: TRP RNA-BINDING ATTENUATION PROTEIN
G: TRP RNA-BINDING ATTENUATION PROTEIN
H: TRP RNA-BINDING ATTENUATION PROTEIN
I: TRP RNA-BINDING ATTENUATION PROTEIN
J: TRP RNA-BINDING ATTENUATION PROTEIN
K: TRP RNA-BINDING ATTENUATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,28223
Polymers90,83111
Non-polymers2,45112
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
W: SINGLE STRANDED RNA (55-MER)
L: TRP RNA-BINDING ATTENUATION PROTEIN
M: TRP RNA-BINDING ATTENUATION PROTEIN
N: TRP RNA-BINDING ATTENUATION PROTEIN
O: TRP RNA-BINDING ATTENUATION PROTEIN
P: TRP RNA-BINDING ATTENUATION PROTEIN
Q: TRP RNA-BINDING ATTENUATION PROTEIN
R: TRP RNA-BINDING ATTENUATION PROTEIN
S: TRP RNA-BINDING ATTENUATION PROTEIN
T: TRP RNA-BINDING ATTENUATION PROTEIN
U: TRP RNA-BINDING ATTENUATION PROTEIN
V: TRP RNA-BINDING ATTENUATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,23823
Polymers108,99112
Non-polymers2,24611
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.970, 111.670, 138.680
Angle α, β, γ (deg.)90.00, 117.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain SINGLE STRANDED RNA (55-MER)


Mass: 18159.916 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: IN-VITRO TRANSCRIPTION
#2: Protein ...
TRP RNA-BINDING ATTENUATION PROTEIN


Mass: 8257.377 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: PTZSTMTRB / Production host: Escherichia coli (E. coli) / Strain (production host): SG62052/PGP1-2 / References: UniProt: Q9X6J6
#3: Chemical...
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1264 / 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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 2000 MONOMETHYL ETHER, TRIETHANOLAMINE, MGCL2, K-GLUTAMATE, K-PHOSPHATE, L- TRYPTOPHAN, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
250 mMpotassium phosphate1drop
37.5 mML-tryptophan1drop
40.2 Mpotassium glutamate1reservoir
550 mMtriethanolamine1reservoir
610 mM1reservoirMgCl2
79-12 %mPEG20001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 1544402 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.396 / % possible all: 71.7
Reflection
*PLUS
Num. obs: 154404
Reflection shell
*PLUS
% possible obs: 71.7 % / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.9→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1545 -RANDOM
Rwork0.188 ---
all0.23 154402 --
obs0.23 152857 96.4 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11912 1210 345 1264 14731
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0260.04

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