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- PDB-8t5y: Structure of Rhodococcus sp. USK13 DarR(K44A)-cAMP complex -

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Basic information

Entry
Database: PDB / ID: 8t5y
TitleStructure of Rhodococcus sp. USK13 DarR(K44A)-cAMP complex
ComponentsDarR
KeywordsTRANSCRIPTION / cAMP / DarR / mycobacteria / TetR / TFR
Function / homologyADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
Function and homology information
Biological speciesRhodococcus sp. USK13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsSchumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: Nat Commun / Year: 2023
Title: Structures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding.
Authors: Schumacher, M.A. / Lent, N. / Chen, V.B. / Salinas, R.
History
DepositionJun 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7382
Polymers23,4081
Non-polymers3291
Water4,594255
1
A: DarR
hetero molecules

A: DarR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4754
Polymers46,8172
Non-polymers6582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4090 Å2
ΔGint-7 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.409, 60.510, 84.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

21A-768-

HOH

31A-841-

HOH

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Components

#1: Protein DarR


Mass: 23408.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. USK13 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 800 mM Succinic acid pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→49.2 Å / Num. obs: 543824 / % possible obs: 100 % / Redundancy: 15.4 % / CC1/2: 1 / Rpim(I) all: 0.02 / Rsym value: 0.054 / Net I/σ(I): 22.5
Reflection shellResolution: 1.44→1.46 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2153 / CC1/2: 0.743 / Rpim(I) all: 0.433 / Rsym value: 0.988

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→49.2 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 2000 4.66 %
Rwork0.1862 --
obs0.1866 42881 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 22 255 1833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.892
X-RAY DIFFRACTIONf_dihedral_angle_d9.578245
X-RAY DIFFRACTIONf_chiral_restr0.064254
X-RAY DIFFRACTIONf_plane_restr0.008294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.480.25911410.24042885X-RAY DIFFRACTION100
1.48-1.520.25311410.22382883X-RAY DIFFRACTION100
1.52-1.560.23611400.21022856X-RAY DIFFRACTION100
1.56-1.610.20981400.2042878X-RAY DIFFRACTION100
1.61-1.670.29551420.23832889X-RAY DIFFRACTION100
1.67-1.740.27651420.22652892X-RAY DIFFRACTION100
1.74-1.810.22391410.20262902X-RAY DIFFRACTION100
1.81-1.910.24751420.21192894X-RAY DIFFRACTION100
1.91-2.030.22931420.20892904X-RAY DIFFRACTION100
2.03-2.190.19381420.19092913X-RAY DIFFRACTION100
2.19-2.410.19591440.18332929X-RAY DIFFRACTION100
2.41-2.750.20631440.18052945X-RAY DIFFRACTION100
2.75-3.470.17371450.17792982X-RAY DIFFRACTION100
3.47-49.20.16831540.16793129X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.6438 Å / Origin y: 9.9586 Å / Origin z: 20.337 Å
111213212223313233
T0.1255 Å2-0.0044 Å2-0.0059 Å2-0.1248 Å20.0062 Å2--0.1948 Å2
L0.4027 °2-0.2698 °2-0.2598 °2-0.78 °20.8394 °2--3.0386 °2
S0.0295 Å °-0.0277 Å °0.0273 Å °-0.016 Å °-0.035 Å °0.036 Å °-0.0809 Å °-0.0063 Å °0.0035 Å °
Refinement TLS groupSelection details: all

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