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- PDB-3aqt: CRYSTAL STRUCTURE OF RolR (NCGL1110) complex WITH ligand RESORCINOL -

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Basic information

Entry
Database: PDB / ID: 3aqt
TitleCRYSTAL STRUCTURE OF RolR (NCGL1110) complex WITH ligand RESORCINOL
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


: / 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
RESORCINOL / Transcriptional regulator
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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 1.2Nov 6, 2013Group: Experimental preparation
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterial regulatory proteins, tetR family
B: Bacterial regulatory proteins, tetR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6874
Polymers54,4672
Non-polymers2202
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-20 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.120, 167.120, 167.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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


Mass: 27233.596 Da / Num. of mol.: 2
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): B834 BL21(DE3) / References: UniProt: Q8NR95
#2: Chemical ChemComp-RCO / RESORCINOL / 1,3-BENZENEDIOL / 1,3-DIHYDROXYBENZENE / Resorcinol


Mass: 110.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.57 Å3/Da / Density % sol: 65.55 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2M SODIUM CHLORIDE, pH 4.60, 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: 0.9795, 0.9797, 0.9644
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2006
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.96441
ReflectionResolution: 2.17→50 Å / Num. all: 26971 / Num. obs: 26929 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 53.7 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 7.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1240 4.6 %RANDOM
Rwork0.212 ---
obs0.212 25555 94.7 %-
all-26971 --
Solvent computationBsol: 40.81 Å2
Displacement parametersBiso mean: 47.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 16 159 3190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 5.4
RfactorNum. reflection% reflection
Rfree0.271 219 -
Rwork0.235 --
obs-3834 91.1 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2RES.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER_REP.PARAM

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