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- PDB-5ojx: Crystal structure of regulator protein 2 (PamR2) from the pamamyc... -

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Basic information

Entry
Database: PDB / ID: 5ojx
TitleCrystal structure of regulator protein 2 (PamR2) from the pamamycin biosynthetic gene cluster of Streptomyces alboniger
ComponentsTetR family transcription regulator
KeywordsTRANSCRIPTION / transcription regulator / TetR family transcription regulator / Streptomyces alboniger / regulator protein 2 / pamamycin biosynthesis
Function / homology
Function and homology information


response to antibiotic / negative regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function
Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A ...Tetracycline transcriptional regulator, TetR / Tetracycline repressor TetR, C-terminal / Tetracyclin repressor-like, C-terminal domain / Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TetR family transcription regulator
Similarity search - Component
Biological speciesStreptomyces alboniger (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchmelz, S. / Rebets, Y. / Luzhetskyy, A. / Scrima, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz AssociationVH-NG-727 Germany
CitationJournal: Metab. Eng. / Year: 2018
Title: Design, development and application of whole-cell based antibiotic-specific biosensor.
Authors: Rebets, Y. / Schmelz, S. / Gromyko, O. / Tistechok, S. / Petzke, L. / Scrima, A. / Luzhetskyy, A.
History
DepositionJul 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TetR family transcription regulator


Theoretical massNumber of molelcules
Total (without water)28,2511
Polymers28,2511
Non-polymers00
Water32418
1
A: TetR family transcription regulator

A: TetR family transcription regulator


Theoretical massNumber of molelcules
Total (without water)56,5012
Polymers56,5012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4840 Å2
ΔGint-49 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.270, 56.030, 39.270
Angle α, β, γ (deg.)90.000, 97.990, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TetR family transcription regulator / Pamamycin regulator protein 2


Mass: 28250.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces alboniger (bacteria) / Gene: pamR2, SALB_00464 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D3RJT7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.89 Å3/Da / Density % sol: 35.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 5mg/mL PamR2 150 mM NaCl 722mM tri-Lithium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→38.889 Å / Num. obs: 12407 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.288 % / Biso Wilson estimate: 48.83 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.041 / Χ2: 1.012 / Net I/σ(I): 20.02
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.24.4730.7171.8616140.7080.816100
2.2-2.34.4660.4812.8713240.850.54799.9
2.3-2.44.4860.3214.1311370.9340.365100
2.4-2.54.390.2225.879670.9630.25399.9
2.5-34.1480.10311.8730760.9930.11899.5
3-44.2920.03135.6324680.9990.03599.7
4-54.080.01956.598820.9990.02299
5-63.7540.0254.263860.9990.02398.5
6-104.3010.01564.244350.9990.01798.9
10-38.8893.8810.01667.8911810.01993.7

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDS20170615data reduction
XSCALE20170615data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y30

2y30


Resolution: 2.1→38.889 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.57
RfactorNum. reflection% reflection
Rfree0.2766 621 5.01 %
Rwork0.2273 --
obs0.2298 12402 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.48 Å2 / Biso mean: 57.1754 Å2 / Biso min: 33.3 Å2
Refinement stepCycle: final / Resolution: 2.1→38.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 0 18 1652
Biso mean---49.8 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071672
X-RAY DIFFRACTIONf_angle_d0.9122273
X-RAY DIFFRACTIONf_chiral_restr0.046251
X-RAY DIFFRACTIONf_plane_restr0.006294
X-RAY DIFFRACTIONf_dihedral_angle_d19.136997
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.31140.36961550.31129383093100
2.3114-2.64580.3341540.287329283082100
2.6458-3.33310.41711550.28372937309299
3.3331-38.89580.21671570.18862978313599

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