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- PDB-3bjb: Crystal structure of a TetR transcriptional regulator from Rhodoc... -

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Basic information

Entry
Database: PDB / ID: 3bjb
TitleCrystal structure of a TetR transcriptional regulator from Rhodococcus sp. RHA1
ComponentsProbable transcriptional regulator, TetR family protein
KeywordsTRANSCRIPTION REGULATOR / APC7331 / TetR / Rhodococcus sp. RHA1 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
HTH-type transcriptional repressor KstR, C-terminal / Tetracyclin repressor-like, C-terminal domain / : / Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Probable transcriptional regulator, TetR family protein
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsTan, K. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a TetR transcriptional regulator from Rhodococcus sp. RHA1.
Authors: Tan, K. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionDec 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Probable transcriptional regulator, TetR family protein
B: Probable transcriptional regulator, TetR family protein
C: Probable transcriptional regulator, TetR family protein
D: Probable transcriptional regulator, TetR family protein
E: Probable transcriptional regulator, TetR family protein
F: Probable transcriptional regulator, TetR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,12227
Polymers138,1056
Non-polymers2,01721
Water32418
1
A: Probable transcriptional regulator, TetR family protein
B: Probable transcriptional regulator, TetR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,80310
Polymers46,0352
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
MethodPISA
2
C: Probable transcriptional regulator, TetR family protein
D: Probable transcriptional regulator, TetR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6118
Polymers46,0352
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
MethodPISA
3
E: Probable transcriptional regulator, TetR family protein
F: Probable transcriptional regulator, TetR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7079
Polymers46,0352
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.767, 93.767, 314.912
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
Probable transcriptional regulator, TetR family protein


Mass: 23017.479 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: RHA1_ro05814 / Plasmid: p15Tv Lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q0S4E5
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.5M Ammonnium sulfate, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899, 0.97918
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978991
20.979181
ReflectionResolution: 2.5→32.46 Å / Num. all: 48913 / Num. obs: 48913 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 27.8
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.8 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→32.46 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 25.035 / SU ML: 0.251 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.487 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27762 2468 5.1 %RANDOM
Rwork0.23173 ---
obs0.23403 46259 98.08 %-
all-46259 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.869 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8306 0 105 18 8429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.81.97811511
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4351060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75122.513374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.087151488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.25315101
X-RAY DIFFRACTIONr_chiral_restr0.1370.21353
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026231
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2570.24294
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.25788
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.35125469
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12738586
X-RAY DIFFRACTIONr_scbond_it1.42623299
X-RAY DIFFRACTIONr_scangle_it2.08432925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 170 -
Rwork0.295 2870 -
obs--84.59 %
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)
11.82841.28931.61727.82132.30233.0681-0.03610.0243-0.55880.79110.5853-0.43620.94650.4686-0.5492-0.00750.2228-0.0635-0.1019-0.04090.003591.78324.857158.172
21.24190.01840.67543.24892.32393.77130.131-0.0909-0.04790.1396-0.40550.57120.2262-1.05710.2745-0.1045-0.13550.00850.0346-0.043-0.033969.25631.134148.117
33.1601-2.0215-1.27712.42210.91062.4804-0.00540.12080.1418-0.124-0.02930.1972-0.3097-0.14380.0347-0.23280.0254-0.0245-0.3711-0.0095-0.178876.98859.826177.935
41.17730.79541.07563.682-0.12865.45340.06560.0366-0.2107-0.0364-0.07550.68291.1959-0.70170.00990.1201-0.0578-0.0508-0.20.0377-0.015766.71240.291187.827
54.072-3.4110.24613.6303-0.00151.64820.13960.40940.6992-0.511-0.1577-0.6844-0.35340.21510.01820.01540.11350.0007-0.2310.0141-0.024154.19794.18176.364
62.54990.42971.58894.93440.49192.98910.2929-0.5292-0.4070.3325-0.18040.64840.2275-0.8146-0.1125-0.14120.00470.0098-0.12720.0019-0.075440.59787.392196.023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 20117 - 203
2X-RAY DIFFRACTION2BB16 - 20118 - 203
3X-RAY DIFFRACTION3CC19 - 20221 - 204
4X-RAY DIFFRACTION4DD21 - 20223 - 204
5X-RAY DIFFRACTION5EE15 - 20217 - 204
6X-RAY DIFFRACTION6FF16 - 20218 - 204

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