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- PDB-3aqs: Crystal structure of RolR (NCGL1110) without ligand -

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Basic information

Entry
Database: PDB / ID: 3aqs
TitleCrystal structure of RolR (NCGL1110) without ligand
ComponentsBacterial regulatory proteins, tetR family
KeywordsTRANSCRIPTION REGULATOR / HELIX-TURN-HELIX / ALL ALPHA / TRANSCRIPTION / TRANSCRIPTION REGULATION / all helix / TetR family / transcriptional repressor / resorcinol binding / DNA binding
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
: / 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
Transcriptional regulator
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsLi, D.F. / Zhang, N. / Hou, Y.J. / Liu, S.J. / Wang, D.C.
CitationJournal: Plos One / Year: 2011
Title: Crystal structures of the transcriptional repressor RolR reveals a novel recognition mechanism between inducer and regulator.
Authors: Li, D.F. / Zhang, N. / Hou, Y.J. / Huang, Y. / Hu, Y. / Zhang, Y. / Liu, S.J. / Wang, D.C.
History
DepositionNov 18, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterial regulatory proteins, tetR family
B: Bacterial regulatory proteins, tetR family
C: Bacterial regulatory proteins, tetR family
D: Bacterial regulatory proteins, tetR family


Theoretical massNumber of molelcules
Total (without water)107,6214
Polymers107,6214
Non-polymers00
Water00
1
A: Bacterial regulatory proteins, tetR family
B: Bacterial regulatory proteins, tetR family


Theoretical massNumber of molelcules
Total (without water)53,8112
Polymers53,8112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-19 kcal/mol
Surface area15780 Å2
MethodPISA
2
C: Bacterial regulatory proteins, tetR family
D: Bacterial regulatory proteins, tetR family


Theoretical massNumber of molelcules
Total (without water)53,8112
Polymers53,8112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-18 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.950, 152.950, 117.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein
Bacterial regulatory proteins, tetR family / Transcriptional regulator


Mass: 26905.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032 / Gene: cg1308, Cgl1157, ncgl1110 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8NR95

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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: 3.19 Å3/Da / Density % sol: 61.47 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 3M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2007
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→108.46 Å / Num. all: 16716 / Num. obs: 16353 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.166 / Rsym value: 0.166 / Net I/σ(I): 13
Reflection shellResolution: 3.6→3.79 Å / Redundancy: 5 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2238 / Rsym value: 0.451 / % possible all: 93.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→93.17 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2239647.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1619 9.9 %RANDOM
Rwork0.22 ---
obs0.22 16348 97.8 %-
all-16716 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.8428 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 103 Å2
Baniso -1Baniso -2Baniso -3
1-13.32 Å20 Å20 Å2
2--13.32 Å20 Å2
3----26.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 3.6→93.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 0 0 5690
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.6→3.83 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 223 8.8 %
Rwork0.287 2309 -
obs-2309 93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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