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- PDB-1wap: TRP RNA-BINDING ATTENUATION PROTEIN IN COMPLEX WITH L-TRYPTOPHAN -

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Basic information

Entry
Database: PDB / ID: 1wap
TitleTRP RNA-BINDING ATTENUATION PROTEIN IN COMPLEX WITH L-TRYPTOPHAN
ComponentsTRP RNA-BINDING ATTENUATION PROTEIN
KeywordsRNA-BINDING ATTENUATION PROTEIN / TRP OPERON / BACILLUS SUBTILIS
Function / homology
Function and homology information


positive regulation of termination of DNA-templated transcription / negative regulation of translational initiation / DNA-templated transcription termination / RNA 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 / Transcription attenuation protein MtrB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsAntson, A.A. / Dodson, E.J. / Gollnick, P.
Citation
#1: Journal: J.Mol.Biol. / Year: 1994
Title: 11-Fold Symmetry of the Trp RNA-Binding Attenuation Protein (Trap)from Bacillus Subtilis Determined by X-Ray Analysis
Authors: Antson, A.A. / Brzozowski, A.M. / Dodson, E.J. / Dauter, Z. / Wilson, K.S. / Kurecki, T. / Otridge, J. / Gollnick, P.
History
DepositionFeb 3, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 29, 2014Group: Derived calculations
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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: 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)188,04944
Polymers183,55722
Non-polymers4,49322
Water36,4982026
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)94,02522
Polymers91,77811
Non-polymers2,24611
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24430 Å2
ΔGint-102 kcal/mol
Surface area27110 Å2
MethodPISA
2
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)94,02522
Polymers91,77811
Non-polymers2,24611
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24680 Å2
ΔGint-99 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.910, 114.440, 105.670
Angle α, β, γ (deg.)90.00, 117.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11K-133-

HOH

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Components

#1: Protein ...
TRP RNA-BINDING ATTENUATION PROTEIN


Mass: 8343.479 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Cell line: BG2087 / Gene: MTRB / Plasmid: PTZMTRAB / Gene (production host): MTRB / Production host: Escherichia coli (E. coli) / Strain (production host): SG62052/PGP1-2 / References: UniProt: P19466
#2: Chemical...
ChemComp-TRP / TRYPTOPHAN


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


Mass: 18.015 Da / Num. of mol.: 2026 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal grow
*PLUS
Method: unknown

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.93
DetectorType: MARRESEARCH / Date: Jun 16, 1994
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 147134 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. measured all: 147134 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
PROLSQrefinement
DENZOdata reduction
RefinementResolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.225 --
Rwork0.178 --
obs0.178 147134 97.5 %
Displacement parametersBiso mean: 20.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11478 0 330 2026 13834
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0390.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2471.5
X-RAY DIFFRACTIONp_mcangle_it1.9172.5
X-RAY DIFFRACTIONp_scbond_it5.0734
X-RAY DIFFRACTIONp_scangle_it7.5686
X-RAY DIFFRACTIONp_plane_restr0.0080.02
X-RAY DIFFRACTIONp_chiral_restr0.1720.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.6845
X-RAY DIFFRACTIONp_staggered_tor16.0810
X-RAY DIFFRACTIONp_orthonormal_tor36.0515
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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