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- PDB-9ny7: Crystal structure of the ribose operon repressor, RbsR, bound to ... -

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Basic information

Entry
Database: PDB / ID: 9ny7
TitleCrystal structure of the ribose operon repressor, RbsR, bound to ribose
ComponentsRibose operon repressor
KeywordsDNA BINDING PROTEIN / ribose operon repressor / RbsR
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
beta-D-ribopyranose / Ribose operon repressor
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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 repressor
D: Ribose operon repressor
E: Ribose operon repressor
F: Ribose operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,53512
Polymers219,6346
Non-polymers9016
Water7,584421
1
A: Ribose operon repressor
B: Ribose operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5124
Polymers73,2112
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-6 kcal/mol
Surface area25160 Å2
MethodPISA
2
C: Ribose operon repressor
hetero molecules

E: Ribose operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5124
Polymers73,2112
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area4130 Å2
ΔGint-8 kcal/mol
Surface area22630 Å2
MethodPISA
3
D: Ribose operon repressor
hetero molecules

D: Ribose operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5124
Polymers73,2112
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4020 Å2
ΔGint-6 kcal/mol
Surface area21800 Å2
MethodPISA
4
F: Ribose operon repressor
hetero molecules

F: Ribose operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5124
Polymers73,2112
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4290 Å2
ΔGint-5 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.461, 87.353, 130.942
Angle α, β, γ (deg.)90.000, 100.378, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ribose operon repressor


Mass: 36605.695 Da / Num. of mol.: 6
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: Sugar
ChemComp-RIP / beta-D-ribopyranose / beta-D-ribose / D-ribose / ribose / RIBOSE(PYRANOSE FORM)


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DRibpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribopyranoseCOMMON NAMEGMML 1.0
b-D-RibpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.2 M sodium malonate (pH 4.0) 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: 0.979493 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: 0.979493 Å / Relative weight: 1
ReflectionResolution: 2.07→33.82 Å / Num. obs: 72942 / % possible obs: 92.1 % / Redundancy: 3.5 % / CC1/2: 0.985 / Rpim(I) all: 0.118 / Net I/σ(I): 4.8
Reflection shellResolution: 2.07→2.367 Å / Num. unique obs: 3646 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
REFMAC5.8refinement
xia2data reduction
Aimlessdata scaling
STARANISOdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→33.82 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 15.337 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.258 / 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
Rfree0.23438 3661 5 %RANDOM
Rwork0.19147 ---
obs0.19361 70230 61.43 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.886 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.13 Å2
2--0.34 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.07→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13378 0 60 421 13859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01713703
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613057
X-RAY DIFFRACTIONr_angle_refined_deg1.2471.8218602
X-RAY DIFFRACTIONr_angle_other_deg0.4381.55930048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785.3131819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.553102367
X-RAY DIFFRACTIONr_chiral_restr0.0610.22134
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023091
X-RAY DIFFRACTIONr_mcbond_it5.5652.2336835
X-RAY DIFFRACTIONr_mcbond_other5.5652.2336835
X-RAY DIFFRACTIONr_mcangle_it8.034.0058535
X-RAY DIFFRACTIONr_mcangle_other8.034.0058536
X-RAY DIFFRACTIONr_scbond_it7.9042.8156868
X-RAY DIFFRACTIONr_scbond_other7.9042.8156869
X-RAY DIFFRACTIONr_scangle_other10.9054.90410068
X-RAY DIFFRACTIONr_long_range_B_refined12.81723.7514992
X-RAY DIFFRACTIONr_long_range_B_other12.83223.4214916
LS refinement shellResolution: 2.07→2.122 Å
RfactorNum. reflection% reflection
Rfree0.422 3 -
Rwork0.354 48 -
obs--0.58 %
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)
12.53731.95760.15752.590.42850.82760.2354-0.2136-0.03350.2906-0.1197-0.2654-0.10650.2454-0.11570.1116-0.05480.00230.1106-0.01760.06823.103-2.19369.048
22.25750.73931.08350.73480.39041.1705-0.09270.23570.259-0.04450.0651-0.1579-0.16720.20530.02760.1699-0.02210.02710.08890.0120.170536.5285.37342.71
32.15251.73220.15222.26320.40120.82420.1325-0.1823-0.01520.2016-0.0548-0.1864-0.07070.2015-0.07770.0878-0.01740.0060.0757-0.01560.050635.143-6.755.24
42.959-0.71990.50642.5453-0.69491.3957-0.0178-0.5475-0.91650.22170.17330.14520.3768-0.1788-0.15550.1966-0.0119-0.01680.15810.14560.361181.345-13.52411.761
52.9625-0.98211.53730.8845-0.6041.4461-0.141-0.20820.25070.10580.12050.0498-0.1614-0.09550.02050.12180.03350.01370.033-0.01090.066146.22-44.46120.656
61.64070.79120.02353.13480.3741.4867-0.11160.317-0.6454-0.28160.175-0.30030.5050.0826-0.06340.2337-0.00350.01350.1037-0.08830.311983.905-9.06152.37
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 330
2X-RAY DIFFRACTION2B1 - 330
3X-RAY DIFFRACTION3C53 - 330
4X-RAY DIFFRACTION4D58 - 330
5X-RAY DIFFRACTION5E52 - 330
6X-RAY DIFFRACTION6F58 - 330

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