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- PDB-3zzq: Engineered 12-subunit Bacillus subtilis trp RNA-binding attenuati... -

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Basic information

Entry
Database: PDB / ID: 3zzq
TitleEngineered 12-subunit Bacillus subtilis trp RNA-binding attenuation protein (TRAP)
ComponentsTRANSCRIPTION ATTENUATION PROTEIN MTRB
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / PROTEIN ENGINEERING
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChen, C. / Smits, C. / Dodson, G.G. / Shevtsov, M.B. / Merlino, N. / Gollnick, P. / Antson, A.A.
CitationJournal: Plos One / Year: 2011
Title: How to Change the Oligomeric State of a Circular Protein Assembly: Switch from 11-Subunit to 12-Subunit Trap Suggests a General Mechanism
Authors: Chen, C. / Smits, C. / Dodson, G.G. / Shevtsov, M.B. / Merlino, N. / Gollnick, P. / Antson, A.A.
History
DepositionSep 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Oct 19, 2016Group: Other
Revision 1.3Dec 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,29718
Polymers42,8476
Non-polymers2,45112
Water5,441302
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,59536
Polymers85,69312
Non-polymers4,90124
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area26770 Å2
ΔGint-94.6 kcal/mol
Surface area29770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.348, 146.348, 146.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11C-2007-

HOH

21F-2005-

HOH

31F-2006-

HOH

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Components

#1: Protein
TRANSCRIPTION ATTENUATION PROTEIN MTRB / TRP RNA-BINDING ATTENUATION PROTEIN / TRAP / TRYPTOPHAN RNA-BINDING ATTENUATOR PROTEIN


Mass: 7141.097 Da / Num. of mol.: 6 / Fragment: RESIDUES 7-71
Source method: isolated from a genetically manipulated source
Details: THE LAST FOUR RESIDUES ARE REMOVED IN B.SUBTILIS TRAP. K71STOP CODON
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P19466
#2: Chemical
ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.68 Å3/Da / Density % sol: 54.2 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 51357 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 25.4 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 42.9
Reflection shellResolution: 1.75→1.79 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0058refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAW

1qaw


Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.576 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 1030 2 %RANDOM
Rwork0.17272 ---
obs0.17307 51357 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.549 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 180 302 3494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223380
X-RAY DIFFRACTIONr_bond_other_d0.0010.022218
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.9354594
X-RAY DIFFRACTIONr_angle_other_deg0.88535467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6595429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71124.539152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43215617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9061514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 78 -
Rwork0.192 3760 -
obs--100 %
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)
11.9897-0.08330.48170.2372-0.14220.2347-0.0555-0.0948-0.10370.02120.0170.0016-0.0063-0.02020.03850.06180.01670.01690.02540.01060.0694-6.4553-27.5941-55.1534
20.8949-0.69920.5851.092-0.5911.091-0.0746-0.00820.00110.0850.0540.11410.0555-0.07370.02060.0552-0.00070.02660.0289-0.00050.0467-19.4541-20.501-55.1892
30.1361-0.33020.181.3574-0.76960.9669-0.0375-0.00670.01180.10240.03430.1448-0.0415-0.02290.00320.03970.00080.01320.05130.00090.0747-27.1347-8.0244-55.1721
40.16930.0834-0.08642.0383-0.55240.31010.0073-0.02910.02430.0966-0.04930.1106-0.0060.00470.0420.0248-0.01490.01070.0616-0.01490.0568-27.58916.5368-55.2805
50.89860.6239-0.44770.9861-0.45830.85290.0467-0.09830.10160.0027-0.07590.02-0.0188-0.03570.02930.0233-0.0021-0.0020.0569-0.0260.0427-20.545519.4664-55.1714
62.04640.4828-0.82020.351-0.03640.46980.0593-0.08330.15240.0029-0.0281-0.0008-0.01240.0087-0.03120.05710.00150.01060.0304-0.02220.0831-8.063427.1604-55.1703
70.2080.0302-0.02030.44730.02890.10530.0006-0.01030.00890.0089-0.01860.0874-0.008-0.01960.0180.0413-0.00080.0050.0649-0.00610.042-20.78132.2179-59.1739
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 91
2X-RAY DIFFRACTION2B7 - 91
3X-RAY DIFFRACTION3C7 - 91
4X-RAY DIFFRACTION4D7 - 91
5X-RAY DIFFRACTION5E7 - 91
6X-RAY DIFFRACTION6F7 - 91
7X-RAY DIFFRACTION7A2001 - 2005
8X-RAY DIFFRACTION7A2007
9X-RAY DIFFRACTION7A2009 - 2025
10X-RAY DIFFRACTION7A2027 - 2054
11X-RAY DIFFRACTION7B2001 - 2007
12X-RAY DIFFRACTION7B2009 - 2028
13X-RAY DIFFRACTION7B2029 - 2051
14X-RAY DIFFRACTION7C2001 - 2006
15X-RAY DIFFRACTION7C2009 - 2055
16X-RAY DIFFRACTION7D2001 - 2020
17X-RAY DIFFRACTION7D2022 - 2047
18X-RAY DIFFRACTION7E2001 - 2008
19X-RAY DIFFRACTION7E2010 - 2047
20X-RAY DIFFRACTION7F2001 - 2005
21X-RAY DIFFRACTION7F2007 - 2009
22X-RAY DIFFRACTION7F2011 - 2023
23X-RAY DIFFRACTION7F2025 - 2027
24X-RAY DIFFRACTION7F2029 - 2048

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