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- PDB-8vst: Rns mutant H20A/R75A -

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Basic information

Entry
Database: PDB / ID: 8vst
TitleRns mutant H20A/R75A
ComponentsRegulatory protein Rns
KeywordsTRANSCRIPTION / AraC homolog
Function / homology
Function and homology information


fatty acid binding / sequence-specific DNA binding / DNA-binding transcription factor activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / Helix-turn-helix domain / DNA binding HTH domain, AraC-type / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA-binding dual transcriptional regulator Rns
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTolbert, J.D. / Midgett, C.R. / Kull, F.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Mutant Structure of Rns H20A
Authors: Tolbert, J.D. / Kull, F.J.
History
DepositionJan 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein Rns
B: Regulatory protein Rns


Theoretical massNumber of molelcules
Total (without water)61,4332
Polymers61,4332
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-11 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.650, 97.290, 136.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 8 through 92 or resid 104 through 263))
d_2ens_1(chain "B" and resid 8 through 263)

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLUTYRTYRAA8 - 928 - 92
d_12SERSERLYSLYSAA104 - 263104 - 263
d_21GLUGLULYSLYSBB8 - 2638 - 263

NCS oper: (Code: givenMatrix: (-0.999298424015, 0.0372138856671, 0.00421740149353), (0.0373268642198, 0.998823338469, 0.0309619724393), (-0.00306022373705, 0.0310976726359, -0.999511665658)Vector: 47. ...NCS oper: (Code: given
Matrix: (-0.999298424015, 0.0372138856671, 0.00421740149353), (0.0373268642198, 0.998823338469, 0.0309619724393), (-0.00306022373705, 0.0310976726359, -0.999511665658)
Vector: 47.7465346963, 1.42357286922, -154.633636874)

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Components

#1: Protein Regulatory protein Rns


Mass: 30716.639 Da / Num. of mol.: 2 / Mutation: H20A,R75A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rns / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16114
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M succinnic acid, 14% PEG 3350, 0.03 M glycyl-glycyl-gylcine, 50% v/v DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979351 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979351 Å / Relative weight: 1
ReflectionResolution: 2.4→48.65 Å / Num. obs: 25620 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 59.48 Å2 / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 6.49
Reflection shellResolution: 2.4→2.486 Å / Mean I/σ(I) obs: 0.78 / Num. unique obs: 2499 / CC1/2: 0.383 / CC star: 0.744 / % possible all: 99.84

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→48.65 Å / SU ML: 0.3657 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.2477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2964 1998 7.81 %
Rwork0.2447 23585 -
obs0.2488 25583 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4017 0 0 15 4032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124075
X-RAY DIFFRACTIONf_angle_d1.25825471
X-RAY DIFFRACTIONf_chiral_restr0.0657636
X-RAY DIFFRACTIONf_plane_restr0.0096676
X-RAY DIFFRACTIONf_dihedral_angle_d15.36061551
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.856687780419 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.38451370.36811632X-RAY DIFFRACTION99.77
2.46-2.530.39091420.34621669X-RAY DIFFRACTION99.83
2.53-2.60.37071380.32481636X-RAY DIFFRACTION99.72
2.6-2.680.34791420.30581667X-RAY DIFFRACTION99.67
2.68-2.780.31771430.2851683X-RAY DIFFRACTION99.67
2.78-2.890.29351380.26421641X-RAY DIFFRACTION99.72
2.89-3.020.36771430.28561679X-RAY DIFFRACTION99.67
3.02-3.180.35421420.27561674X-RAY DIFFRACTION99.89
3.18-3.380.27941430.25811681X-RAY DIFFRACTION99.84
3.38-3.640.30541420.2451687X-RAY DIFFRACTION99.84
3.64-4.010.31481440.24841691X-RAY DIFFRACTION99.57
4.01-4.590.28391420.21141687X-RAY DIFFRACTION99.46
4.59-5.780.26281470.2231740X-RAY DIFFRACTION99.68
5.78-48.650.25541550.21161818X-RAY DIFFRACTION99.25

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