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- PDB-2zd0: Crystal structures and thermostability of mutant TRAP3 A5 (ENGINE... -

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Basic information

Entry
Database: PDB / ID: 2zd0
TitleCrystal structures and thermostability of mutant TRAP3 A5 (ENGINEERED TRAP)
ComponentsTranscription attenuation protein mtrB
KeywordsRNA BINDING PROTEIN / LINKER / ARTIFICIAL / ENGINEERED / RING PROTEIN / 12-mer
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 / Transcription attenuation protein MtrB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWatanabe, M. / Mishima, Y. / Yamashita, I. / Park, S.Y. / Tame, J.R.H. / Heddle, J.G.
CitationJournal: Protein Sci. / Year: 2008
Title: Intersubunit linker length as a modifier of protein stability: crystal structures and thermostability of mutant TRAP.
Authors: Watanabe, M. / Mishima, Y. / Yamashita, I. / Park, S.Y. / Tame, J.R. / Heddle, J.G.
History
DepositionNov 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 8, 2017Group: Structure summary
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Transcription attenuation protein mtrB
B: Transcription attenuation protein mtrB
C: Transcription attenuation protein mtrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4516
Polymers25,8383
Non-polymers6133
Water70339
1
A: Transcription attenuation protein mtrB
B: Transcription attenuation protein mtrB
C: Transcription attenuation protein mtrB
hetero molecules

A: Transcription attenuation protein mtrB
B: Transcription attenuation protein mtrB
C: Transcription attenuation protein mtrB
hetero molecules

A: Transcription attenuation protein mtrB
B: Transcription attenuation protein mtrB
C: Transcription attenuation protein mtrB
hetero molecules

A: Transcription attenuation protein mtrB
B: Transcription attenuation protein mtrB
C: Transcription attenuation protein mtrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,80424
Polymers103,35312
Non-polymers2,45112
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area25330 Å2
ΔGint-113 kcal/mol
Surface area30420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.676, 109.676, 36.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsTHE POLYPEPTIDE CHAIN CONTAINS THREE (3) COPIES OF THE TRAP PROTEIN LINKED IN TANDEM, WHICH ARRANGE THEMSELVES TO MAKE A 12-MER RING IN SOLUTION. EACH CHAIN IN THIS MODEL REPRESENTS ONE COPY OF TRAP, NOT A SEPARATE POLYPEPTIDE. THE LINKER PEPTIDES ARE NOT VISIBLE IN THE ELECTRON DENSITY. THE 12MER RINGS ARE ALIGNED WITH THE CRYSTALLOGRAPHIC FOUR-FOLD AXIS. THERE ARE THREE COPIES OF TRAP PRESENT IN THE ASYMMETRIC UNIT. FOR THIS PROTEIN, CALLED T3A5, THE LINKER PEPTIDES CONSIST OF FIVE (5) ALANINE RESIDUES.

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Components

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


Mass: 8612.765 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: NCA 26, ATCC 12980 / Gene: mtrB / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X6J6
#2: Chemical ChemComp-TRP / TRYPTOPHAN


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


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 0.09M CAPS pH 10.5, 30%(w/v) PEG300, 0.15M Ammonium sulfate, 10mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 7, 2006 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 7898 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.048 / Net I/σ(I): 12.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 11.7 / Num. unique all: 744 / Rsym value: 0.246 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EXS

2exs


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.967 / SU ML: 0.185 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.609 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25647 363 4.6 %RANDOM
Rwork0.19691 ---
obs0.19971 7503 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.491 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 45 39 1603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211591
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9272141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1035192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1823.10874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01515283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2981512
X-RAY DIFFRACTIONr_chiral_restr0.0850.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021181
X-RAY DIFFRACTIONr_nbd_refined0.20.2529
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.221
X-RAY DIFFRACTIONr_mcbond_it0.7441.51007
X-RAY DIFFRACTIONr_mcangle_it1.23521562
X-RAY DIFFRACTIONr_scbond_it1.8553664
X-RAY DIFFRACTIONr_scangle_it3.0344.5579
LS refinement shellResolution: 2.497→2.561 Å / Rfactor Rfree error: 0.08 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 22 -
Rwork0.195 511 -
obs-7503 100 %

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