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- PDB-9iib: Crystal structure of NodD-EBD (Effector Binding Domain) in comple... -

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Basic information

Entry
Database: PDB / ID: 9iib
TitleCrystal structure of NodD-EBD (Effector Binding Domain) in complex with hesperetin from Rhizobium leguminosarum bv. vicae 3841
ComponentsLysR family transcriptional regulator
KeywordsTRANSCRIPTION / NodD / LysR transcription factors / Flavonoids / Rhizobia
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Nodulation protein D, PBP2 / : / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-6JP / LysR family transcriptional regulator
Similarity search - Component
Biological speciesRhizobium leguminosarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsRuan, Y. / Dong, S. / Zhang, Y. / Jeremy, M.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32150710527 China
The Ministry of Science and Technology2024YFA0918203 China
Shanghai Science and Technology Commission22JC1410800 China
Basic Research Zone Program of ShanghaiJCYJ-SHFY-2022-012 China
CAS Project for Young Scientists in Basic ResearchYSBR-011 China
CitationJournal: Science / Year: 2026
Title: The molecular basis of the binding and specific activation of rhizobial NodD by flavonoids.
Authors: Ruan, Y. / Dong, S. / Jiang, S. / Wang, Y. / Wu, X. / Zhuang, Y. / Wu, W. / East, A.K. / Xu, P. / Poole, P.S. / Zhang, Y. / Murray, J.D.
History
DepositionJun 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2026Group: 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_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysR family transcriptional regulator
B: LysR family transcriptional regulator
C: LysR family transcriptional regulator
D: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,31812
Polymers99,3204
Non-polymers1,9988
Water1,00956
1
A: LysR family transcriptional regulator
D: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6596
Polymers49,6602
Non-polymers9994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-15 kcal/mol
Surface area17110 Å2
MethodPISA
2
B: LysR family transcriptional regulator
C: LysR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6596
Polymers49,6602
Non-polymers9994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-17 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.420, 197.708, 50.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
LysR family transcriptional regulator


Mass: 24830.012 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum (bacteria) / Gene: GUK36_35585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6P0BW74
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-6JP / (2S)-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-2,3-dihydro-4H-1-benzopyran-4-one


Mass: 302.279 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H14O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Tris-HCl pH 7.5, 0.2 M potassium chloride, 0.05 M magnesium chloride, 10% w/v polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→35.3 Å / Num. obs: 25640 / % possible obs: 99.73 % / Redundancy: 7 % / CC1/2: 0.997 / Net I/σ(I): 16.24
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.75-2.910.34127460.730.4821
2.91-3.110.22325510.8860.3151
3.11-3.360.13422280.950.191
3.36-3.680.08120580.9820.1141
3.68-4.110.05717770.9920.0811
4.11-4.740.03915830.9940.0551
4.74-5.790.03112490.9970.0441
5.79-8.140.039750.9980.0421

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→35.3 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1279 5 %
Rwork0.2208 --
obs0.2224 25594 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→35.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 116 56 6571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116668
X-RAY DIFFRACTIONf_angle_d1.4269065
X-RAY DIFFRACTIONf_dihedral_angle_d16.9412478
X-RAY DIFFRACTIONf_chiral_restr0.0811020
X-RAY DIFFRACTIONf_plane_restr0.0191168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.860.34131410.29032670X-RAY DIFFRACTION99
2.86-2.990.30271420.27792701X-RAY DIFFRACTION100
2.99-3.140.3531430.26862725X-RAY DIFFRACTION100
3.14-3.340.32571420.25792700X-RAY DIFFRACTION100
3.34-3.60.28641430.24852701X-RAY DIFFRACTION100
3.6-3.960.28621420.22542697X-RAY DIFFRACTION100
3.96-4.530.21861430.19312724X-RAY DIFFRACTION100
4.53-5.710.21341420.1872699X-RAY DIFFRACTION100
5.71-35.30.19621410.20522698X-RAY DIFFRACTION99

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