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- PDB-3zzs: Engineered 12-subunit Bacillus stearothermophilus trp RNA-binding... -

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Basic information

Entry
Database: PDB / ID: 3zzs
TitleEngineered 12-subunit Bacillus stearothermophilus trp RNA-binding attenuation protein (TRAP)
ComponentsTRANSCRIPTION ATTENUATION PROTEIN MTRB
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / PROTEIN ENGINEERING
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: 1.49 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 1.2Dec 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: 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
G: TRANSCRIPTION ATTENUATION PROTEIN MTRB
H: TRANSCRIPTION ATTENUATION PROTEIN MTRB
I: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,78418
Polymers64,9469
Non-polymers1,8389
Water17,619978
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)89,04524
Polymers86,59412
Non-polymers2,45112
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area25170 Å2
ΔGint-92.6 kcal/mol
Surface area30650 Å2
MethodPISA
2
D: TRANSCRIPTION ATTENUATION PROTEIN MTRB
E: TRANSCRIPTION ATTENUATION PROTEIN MTRB
F: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules

D: TRANSCRIPTION ATTENUATION PROTEIN MTRB
E: TRANSCRIPTION ATTENUATION PROTEIN MTRB
F: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules

D: TRANSCRIPTION ATTENUATION PROTEIN MTRB
E: TRANSCRIPTION ATTENUATION PROTEIN MTRB
F: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules

D: TRANSCRIPTION ATTENUATION PROTEIN MTRB
E: TRANSCRIPTION ATTENUATION PROTEIN MTRB
F: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,04524
Polymers86,59412
Non-polymers2,45112
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655y+1,-x,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
Buried area24580 Å2
ΔGint-84.3 kcal/mol
Surface area30530 Å2
MethodPISA
3
G: TRANSCRIPTION ATTENUATION PROTEIN MTRB
H: TRANSCRIPTION ATTENUATION PROTEIN MTRB
I: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules

G: TRANSCRIPTION ATTENUATION PROTEIN MTRB
H: TRANSCRIPTION ATTENUATION PROTEIN MTRB
I: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules

G: TRANSCRIPTION ATTENUATION PROTEIN MTRB
H: TRANSCRIPTION ATTENUATION PROTEIN MTRB
I: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules

G: TRANSCRIPTION ATTENUATION PROTEIN MTRB
H: TRANSCRIPTION ATTENUATION PROTEIN MTRB
I: TRANSCRIPTION ATTENUATION PROTEIN MTRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,04524
Polymers86,59412
Non-polymers2,45112
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area24980 Å2
ΔGint-98 kcal/mol
Surface area30120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.203, 110.203, 128.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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


Mass: 7216.196 Da / Num. of mol.: 9 / Fragment: RESIDUES 5-69
Source method: isolated from a genetically manipulated source
Details: THE LAST FIVE RESIDUES ARE REMOVED IN B. STEAROTHERMOPHILUS TRAP E71STOP
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9X6J6
#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 978 / 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: 2.71 Å3/Da / Density % sol: 54.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.49→25 Å / Num. obs: 124338 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.5
Reflection shellResolution: 1.49→1.73 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QAW

1qaw


Resolution: 1.49→25 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.888 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18228 1250 1 %RANDOM
Rwork0.14678 ---
obs0.14713 123011 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.058 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.49→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4581 0 135 978 5694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224964
X-RAY DIFFRACTIONr_bond_other_d0.0010.023313
X-RAY DIFFRACTIONr_angle_refined_deg1.0751.9326739
X-RAY DIFFRACTIONr_angle_other_deg0.93238103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9815634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.42823.447235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.64815896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9921536
X-RAY DIFFRACTIONr_chiral_restr0.050.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021041
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_restr1.22738277
X-RAY DIFFRACTIONr_sphericity_free38.5895467
X-RAY DIFFRACTIONr_sphericity_bonded10.20658676
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 87 -
Rwork0.218 8988 -
obs--99.87 %
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)
10.81180.19290.27910.4725-0.01071.19280.0121-0.0448-0.07280.029-0.0464-0.02010.0140.04710.03430.01480.0019-0.00270.02460.0180.019221.0484-19.8281-0.1665
21.03750.1510.79990.4372-0.03741.53970.0164-0.0557-0.08050.0155-0.01040.010.0441-0.0155-0.0060.01370.00980.01080.02140.01640.02038.1784-27.6451-0.1111
31.27470.00560.70390.4356-0.12091.1668-0.0242-0.1108-0.07910.04040.00660.040.0533-0.04730.01770.02910.00930.02190.0240.0160.0221-6.6995-28.0469-0.0468
40.94140.1977-0.4861.013-0.35381.12960.00830.07510.0152-0.040.00240.0621-0.0103-0.0641-0.01070.01710.0117-0.01340.0205-0.00170.016335.2718-34.3084-12.0597
50.53570.1771-0.12981.1582-0.68161.61-0.00180.0414-0.0167-0.05190.00610.10710.0173-0.1075-0.00430.0160.0119-0.01850.0217-0.01540.028327.6582-47.0165-11.9781
60.51850.01560.1521.3395-0.68831.3408-0.01810.0273-0.0273-0.0870.00510.09870.0565-0.11520.0130.0167-0.0007-0.01510.032-0.02040.029827.0726-61.9361-12.0644
70.8409-0.16110.71010.3902-0.23321.4570.03450.0155-0.0587-0.03030.0007-0.00620.0678-0.0054-0.03520.0249-0.00810.00360.0271-0.01210.0095-15.0423-24.5795-38.3209
81.1371-0.02630.74230.5684-0.04141.54710.01670.0562-0.0789-0.0465-0.0152-0.02930.09820.0352-0.00150.034-0.00670.01470.0189-0.01050.0144-0.8471-28.8158-38.2438
91.00990.30150.59340.74910.47751.5842-0.01590.0768-0.0563-0.010.0136-0.07490.04330.06670.00230.03190.00350.01730.0253-0.0010.017413.7228-25.3576-38.3936
100.0478-0.02130.01630.0322-0.02390.0179-0.0010.0059-0.0054-0.00570.0004-0.00260.0043-0.00150.00070.0394-0.00280.00090.0469-0.00430.035211.6549-33.2332-16.3458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 81
2X-RAY DIFFRACTION2B5 - 81
3X-RAY DIFFRACTION3C5 - 81
4X-RAY DIFFRACTION4D5 - 81
5X-RAY DIFFRACTION5E5 - 81
6X-RAY DIFFRACTION6F5 - 81
7X-RAY DIFFRACTION7G5 - 81
8X-RAY DIFFRACTION8H5 - 81
9X-RAY DIFFRACTION9I5 - 81
10X-RAY DIFFRACTION10A2001 - 2137
11X-RAY DIFFRACTION10B2001 - 2120
12X-RAY DIFFRACTION10C2001 - 2099
13X-RAY DIFFRACTION10D2001 - 2123
14X-RAY DIFFRACTION10E2001 - 2096
15X-RAY DIFFRACTION10F2001 - 2093
16X-RAY DIFFRACTION10G2001 - 2125
17X-RAY DIFFRACTION10H2001 - 2102
18X-RAY DIFFRACTION10I2001 - 2083

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