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- PDB-5h58: Structural and dynamics studies of the TetR family protein, CprB ... -

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Basic information

Entry
Database: PDB / ID: 5h58
TitleStructural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence
Components
  • CprB
  • DNA (5'-D(*AP*GP*GP*C*AP*GP*GP*CP*GP*GP*CP*AP*CP*GP*GP*TP*CP*TP*GP*TP*TP*GP*AP*GP*TP*TP*C)-3')
  • DNA (5'-D(*GP*AP*A*CP*TP*CP*AP*AP*CP*AP*GP*AP*CP*CP*GP*TP*GP*CP*CP*GP*CP*CP*TP*GP*CP*CP*T)-3')
KeywordsTRANSCRIPTION/DNA / TetR-FTR / CprB-DNA complex / quorum sensing / N-terminal / Streptomyces coelicolor / gamma-butyrolactone receptors / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
: / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily ...: / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / 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
DNA / DNA (> 10) / CprB / A-factor receptor homolog
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.991 Å
AuthorsBhukya, H. / Jana, A.K. / Sengupta, N. / Anand, R.
Funding support India, 2items
OrganizationGrant numberCountry
BRNS20150237B02RP00614-BRNS India
IIT Bombay India
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence
Authors: Bhukya, H. / Jana, A.K. / Sengupta, N. / Anand, R.
History
DepositionNov 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CprB
B: CprB
C: CprB
D: CprB
E: DNA (5'-D(*AP*GP*GP*C*AP*GP*GP*CP*GP*GP*CP*AP*CP*GP*GP*TP*CP*TP*GP*TP*TP*GP*AP*GP*TP*TP*C)-3')
F: DNA (5'-D(*GP*AP*A*CP*TP*CP*AP*AP*CP*AP*GP*AP*CP*CP*GP*TP*GP*CP*CP*GP*CP*CP*TP*GP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)111,4746
Polymers111,4746
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-94 kcal/mol
Surface area43920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.810, 149.810, 70.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
CprB


Mass: 23719.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Strain: A3(2) / Gene: cprB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): 'BL21-Gold(DE3)pLysS AG' / References: UniProt: O66122, UniProt: Q7AKF2*PLUS
#2: DNA chain DNA (5'-D(*AP*GP*GP*C*AP*GP*GP*CP*GP*GP*CP*AP*CP*GP*GP*TP*CP*TP*GP*TP*TP*GP*AP*GP*TP*TP*C)-3')


Mass: 8389.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria)
#3: DNA chain DNA (5'-D(*GP*AP*A*CP*TP*CP*AP*AP*CP*AP*GP*AP*CP*CP*GP*TP*GP*CP*CP*GP*CP*CP*TP*GP*CP*CP*T)-3')


Mass: 8207.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptomyces coelicolor A3(2) (bacteria)

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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: 4.06 Å3/Da / Density % sol: 69.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M ammonium acetate, 0.02 M MgCl2.6H2O, 0.05 M HEPES sodium, 5% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9737 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 3.95→50 Å / Num. obs: 15346 / % possible obs: 99.7 % / Redundancy: 3.5 % / Net I/σ(I): 22.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 3.991→40.249 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 32.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2816 1153 7.72 %RANDOM
Rwork0.2166 ---
obs0.2215 14937 99.33 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.991→40.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6030 855 0 0 6885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027088
X-RAY DIFFRACTIONf_angle_d0.5599793
X-RAY DIFFRACTIONf_dihedral_angle_d19.7954119
X-RAY DIFFRACTIONf_chiral_restr0.0361149
X-RAY DIFFRACTIONf_plane_restr0.0031111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9906-4.1720.34961520.26271721X-RAY DIFFRACTION99
4.172-4.39170.3191480.24191738X-RAY DIFFRACTION100
4.3917-4.66650.32551500.24371710X-RAY DIFFRACTION100
4.6665-5.02620.3241460.22071713X-RAY DIFFRACTION99
5.0262-5.53080.30291400.22761730X-RAY DIFFRACTION100
5.5308-6.32850.36941320.26531741X-RAY DIFFRACTION100
6.3285-7.96310.28071460.25071726X-RAY DIFFRACTION99
7.9631-40.2510.21791390.171705X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 28.5623 Å / Origin y: 49.9099 Å / Origin z: -0.0142 Å
111213212223313233
T1.5491 Å20.2143 Å20.116 Å2-1.8444 Å2-0.0809 Å2--1.9014 Å2
L3.6625 °2-2.3526 °20.8398 °2-1.1467 °2-0.5627 °2---0.0998 °2
S0.1456 Å °-0.1408 Å °0.4582 Å °-0.2442 Å °-0.0906 Å °-0.274 Å °0.3071 Å °-0.2163 Å °-0.0443 Å °
Refinement TLS groupSelection details: all

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