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- PDB-3zte: Crystal Structure of the TRP RNA-Binding Attenuation Protein (TRA... -

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Basic information

Entry
Database: PDB / ID: 3zte
TitleCrystal Structure of the TRP RNA-Binding Attenuation Protein (TRAP) from Bacillus Licheniformis.
ComponentsTRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / TRANSCRIPTION FACTORS / TRINUCLEOTIDE REPEATS
Function / homology
Function and homology information


DNA-templated transcription termination / regulation of DNA-templated transcription / 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 LICHENIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsShevtsov, M.B. / Chen, Y. / Gollnick, P. / Antson, A.A.
CitationJournal: To be Published
Title: Crystal Structure of the Trp RNA-Binding Attenuation Protein (Trap) from Bacillus Licheniformis.
Authors: Shevtsov, M.B. / Chen, Y. / Gollnick, P. / Antson, A.A.
History
DepositionJul 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
B: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
C: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
D: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
E: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
F: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
G: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
H: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
I: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
J: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
K: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
L: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
M: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
N: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
O: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
P: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
Q: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
R: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
S: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
T: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
U: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
V: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,44944
Polymers190,95622
Non-polymers4,49322
Water8,503472
1
L: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
M: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
N: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
O: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
P: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
Q: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
R: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
S: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
T: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
U: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
V: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,72422
Polymers95,47811
Non-polymers2,24611
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23810 Å2
ΔGint-72.2 kcal/mol
Surface area30360 Å2
MethodPISA
2
A: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
B: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
C: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
D: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
E: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
F: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
G: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
H: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
I: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
J: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
K: TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,72422
Polymers95,47811
Non-polymers2,24611
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23720 Å2
ΔGint-71.6 kcal/mol
Surface area30320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.427, 145.427, 183.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ...
TRYPTOPHAN OPERON RNA-BINDING ATTENUATION PROTEIN (TRAP) / TRP RNA-BINDING ATTENUATION PROTEIN


Mass: 8679.808 Da / Num. of mol.: 22
Source method: isolated from a genetically manipulated source
Details: 22 L-TRYPTOPHAN MOLECULES ARE BOUND (ONE LIGAND PER SUBUNIT)
Source: (gene. exp.) BACILLUS LICHENIFORMIS (bacteria) / Strain: DSM 13 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q65I22, UniProt: A5A665*PLUS
#2: Chemical...
ChemComp-TRP / TRYPTOPHAN / Tryptophan


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


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsL-TRYPTOPHAN (LTR): THE BOUND L-TRYPTOPHAN ACTIVATES TRAP TO BIND MRNA TRANSCRIPT

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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: 2.55 Å3/Da / Density % sol: 51.7 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7.5
Details: PROTEIN WAS IN BUFFER 50 MM OF POTASSIUM PHOSPHATE; CONCENTRATION 14.7 MG/ML, TEMPERATURE 293K; NO L-TRP WAS ADDED. CRYSTALLISATION CONDITIONS: 0.1 M HEPES PH 7.0, 5% (V/V) TASCIMATE PH 7.0, ...Details: PROTEIN WAS IN BUFFER 50 MM OF POTASSIUM PHOSPHATE; CONCENTRATION 14.7 MG/ML, TEMPERATURE 293K; NO L-TRP WAS ADDED. CRYSTALLISATION CONDITIONS: 0.1 M HEPES PH 7.0, 5% (V/V) TASCIMATE PH 7.0, 10% (W/V) PEG5KMME. CRYOPROTECTION: 15%(W/V) PEG5KMME, 10%(V/V) GLYCEROL.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 15, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 76452 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.1 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAW

1qaw


Resolution: 2.41→44.83 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.863 / SU B: 13.069 / SU ML: 0.303 / Cross valid method: THROUGHOUT / ESU R: 0.543 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.34606 3709 5 %RANDOM
Rwork0.28063 ---
obs0.28401 70030 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.983 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.41→44.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11580 0 330 472 12382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02112082
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7821.97616206
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.67351488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.45525.019536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44152280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5541567
X-RAY DIFFRACTIONr_chiral_restr0.0590.21857
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028872
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7981.57493
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5212074
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.49334589
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0954.54127
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.407→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 218 -
Rwork0.374 4193 -
obs--79.28 %

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