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- PDB-9ny8: Crystal structure of the ribose operon repressor, RbsR, bound to ... -

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Basic information

Entry
Database: PDB / ID: 9ny8
TitleCrystal structure of the ribose operon repressor, RbsR, bound to ribose operon
Components
  • (ribose operon) x 2
  • Ribose operon repressor
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


monosaccharide binding / DNA-binding transcription activator activity / cis-regulatory region sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
Similarity search - Function
LacI-type HTH domain signature. / Transcriptional regulator LacI/GalR-like, sensor domain / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
DNA / DNA (> 10) / Ribose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWells, M.L. / Lu, C. / Sultanov, D. / Weber, K.C. / Gong, Z. / Glasgow, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM135529 United States
CitationJournal: Biorxiv / Year: 2025
Title: Conserved energetic changes drive function in an ancient protein fold.
Authors: Wells, M.L. / Lu, C. / Sultanov, D. / Weber, K.C. / Gong, Z. / Glasgow, A.
History
DepositionMar 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 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: Ribose operon repressor
B: Ribose operon repressor
C: ribose operon
D: ribose operon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9487
Polymers91,6604
Non-polymers2883
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-134 kcal/mol
Surface area34150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.530, 125.530, 122.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ribose operon repressor


Mass: 36605.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rbsR, b3753, JW3732 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ACQ0
#2: DNA chain ribose operon


Mass: 9360.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain ribose operon


Mass: 9088.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium sulfate, 0.1 M bis-tris-propane (pH 6.5), and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.1→43.84 Å / Num. obs: 47896 / % possible obs: 94.1 % / Redundancy: 30.5 % / CC1/2: 0.999 / Rpim(I) all: 0.045 / Net I/σ(I): 15.7
Reflection shellResolution: 2.1→2.33 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2397 / CC1/2: 0.184

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
xia2data reduction
STARANISOdata scaling
Aimlessdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 18.994 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22327 2323 4.9 %RANDOM
Rwork0.19214 ---
obs0.1937 45573 73.51 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.31 Å20 Å2
2--0.63 Å2-0 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5126 1232 15 58 6431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0166691
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165651
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.7159236
X-RAY DIFFRACTIONr_angle_other_deg0.371.55813058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285.299702
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00610909
X-RAY DIFFRACTIONr_chiral_restr0.0450.21064
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026924
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021382
X-RAY DIFFRACTIONr_mcbond_it4.2494.8152643
X-RAY DIFFRACTIONr_mcbond_other4.2494.8142643
X-RAY DIFFRACTIONr_mcangle_it6.1038.673302
X-RAY DIFFRACTIONr_mcangle_other6.1038.673303
X-RAY DIFFRACTIONr_scbond_it5.4145.4084048
X-RAY DIFFRACTIONr_scbond_other5.2765.3984037
X-RAY DIFFRACTIONr_scangle_other7.869.6825917
X-RAY DIFFRACTIONr_long_range_B_refined9.88677.3513112
X-RAY DIFFRACTIONr_long_range_B_other9.88677.3513110
LS refinement shellResolution: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 3 -
Rwork0.375 41 -
obs--0.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8119-0.3678-0.18530.58250.06380.43730.0991-0.01180.31920.00590.02670.0303-0.06350.0638-0.12570.0431-0.03070.06090.0637-0.00670.13365.31-25.811-21.029
21.4552-1.1812-0.17882.0240.10260.25830.0394-0.0428-0.187-0.01410.03240.32120.0739-0.0404-0.07180.0283-0.0151-0.03260.05390.05120.138457.102-40.077-34.367
32.29410.75850.1863.4189-1.57712.94980.0990.24090.60810.24110.35441.0005-0.509-0.9388-0.45350.20450.17410.16920.39480.20220.742719.883-10.232-28.291
42.78321.0898-1.02694.1357-1.49513.9640.10590.18380.58910.2780.31711.1001-0.455-1.1253-0.42310.0670.11590.10840.38650.1620.724519.765-10.961-27.638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 330
2X-RAY DIFFRACTION2B1 - 330
3X-RAY DIFFRACTION3C1 - 30
4X-RAY DIFFRACTION4D1 - 30

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