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- PDB-8vrq: Rns pocket mutant - R75A -

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Basic information

Entry
Database: PDB / ID: 8vrq
TitleRns pocket mutant - R75A
ComponentsRegulatory protein Rns
KeywordsDNA BINDING PROTEIN / Inhibitor / AraC
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 (bacteria)
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: Structure of Rns R75A mutant
Authors: Tolbert, J.D. / Talbot, K.M. / Bollinger, C.M. / Kull, F.J. / Munson, G.P. / Midgett, C.R.
History
DepositionJan 22, 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)61,4512
Polymers61,4512
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-11 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.730, 96.970, 136.590
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 5 through 264)
d_2ens_1(chain "B" and resid 5 through 264)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 5 - 264 / Label seq-ID: 5 - 264

Dom-IDAuth asym-IDLabel asym-ID
d_1BB
d_2AA

NCS oper: (Code: givenMatrix: (-0.999901516599, 0.0111263091384, -0.0085534991755), (0.0114222276165, 0.999309249937, -0.0353631970698), (0.00815412898268, -0.0354574143964, -0.999337921799)Vector: 0. ...NCS oper: (Code: given
Matrix: (-0.999901516599, 0.0111263091384, -0.0085534991755), (0.0114222276165, 0.999309249937, -0.0353631970698), (0.00815412898268, -0.0354574143964, -0.999337921799)
Vector: 0.148289349748, -0.0668030717802, -17.5125609733)

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Components

#1: Protein Regulatory protein Rns


Mass: 30725.604 Da / Num. of mol.: 2 / Mutation: R75A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia (bacteria) / Gene: rns / Production host: Eschenbachia (plant) / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 0.03 M glycyl-glycyl-gylcine, 14% PEG 3350, 0.1 M succinic acid, 30% 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: 0.97864 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 2.4→29.22 Å / Num. obs: 25501 / % possible obs: 99.55 % / Redundancy: 6.4 % / Biso Wilson estimate: 63.71 Å2 / CC1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 7.03
Reflection shellResolution: 2.4→2.48 Å / Num. unique obs: 2497 / CC1/2: 0.395 / % possible all: 99.64

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.22 Å / SU ML: 0.3911 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8817
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2859 1996 7.84 %
Rwork0.2391 23460 -
obs0.2428 25456 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.03 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4137 0 0 15 4152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01044199
X-RAY DIFFRACTIONf_angle_d1.17555636
X-RAY DIFFRACTIONf_chiral_restr0.0608649
X-RAY DIFFRACTIONf_plane_restr0.0093698
X-RAY DIFFRACTIONf_dihedral_angle_d14.4421596
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.32562939092 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.33481390.31821633X-RAY DIFFRACTION99.61
2.46-2.530.41071420.32221655X-RAY DIFFRACTION99.78
2.53-2.60.37341390.32211634X-RAY DIFFRACTION99.94
2.6-2.680.35531410.29941664X-RAY DIFFRACTION99.94
2.68-2.780.35261430.30021671X-RAY DIFFRACTION99.89
2.78-2.890.35651390.30561641X-RAY DIFFRACTION99.94
2.89-3.020.38391420.31961668X-RAY DIFFRACTION99.83
3.02-3.180.30921430.27551676X-RAY DIFFRACTION99.84
3.18-3.380.31551400.24761665X-RAY DIFFRACTION99.89
3.38-3.640.33041430.26191669X-RAY DIFFRACTION99.62
3.64-4.010.28721440.22861693X-RAY DIFFRACTION99.51
4.01-4.590.24271420.20421675X-RAY DIFFRACTION99.24
4.59-5.770.23681460.21471724X-RAY DIFFRACTION99.42
5.77-29.220.24981530.20031792X-RAY DIFFRACTION98.53

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