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- PDB-9x6w: Crystal structure of NodD-EBD (Effector Binding Domain) from Rhiz... -

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Basic information

Entry
Database: PDB / ID: 9x6w
TitleCrystal structure of NodD-EBD (Effector Binding Domain) 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
LysR family transcriptional regulator
Similarity search - Component
Biological speciesRhizobium leguminosarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsRuan, Y. / Dong, S. / Zhang, Y. / Murray, J.
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
DepositionOct 16, 2025Deposition 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
E: LysR family transcriptional regulator
F: LysR family transcriptional regulator
G: LysR family transcriptional regulator
H: LysR family transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)201,6678
Polymers201,6678
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20300 Å2
ΔGint-146 kcal/mol
Surface area75940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.774, 192.774, 153.297
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-414-

HOH

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Components

#1: Protein
LysR family transcriptional regulator


Mass: 25208.416 Da / Num. of mol.: 8 / Fragment: NodD-EBD (Effector Binding Domain)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.0, 0.1 M potassium chloride, 15% w/v polyethylene glycol 5,000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 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: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.298→50 Å / Num. obs: 49459 / % possible obs: 99.12 % / Redundancy: 7.75 % / Biso Wilson estimate: 84.88 Å2 / CC1/2: 0.9906 / Rmerge(I) obs: 0.1558 / Net I/σ(I): 13.83
Reflection shellResolution: 3.298→3.416 Å / Num. unique obs: 49459 / CC1/2: 0.727

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
autoPXdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→48.86 Å / SU ML: 0.3853 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2528 1985 4.02 %
Rwork0.2219 47426 -
obs0.2232 49411 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.77 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12840 0 0 103 12943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011713137
X-RAY DIFFRACTIONf_angle_d1.270517883
X-RAY DIFFRACTIONf_chiral_restr0.05652076
X-RAY DIFFRACTIONf_plane_restr0.00992319
X-RAY DIFFRACTIONf_dihedral_angle_d12.87384801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.380.34251250.32373073X-RAY DIFFRACTION89.83
3.38-3.470.33081420.27933363X-RAY DIFFRACTION100
3.47-3.570.30161460.28243402X-RAY DIFFRACTION100
3.57-3.690.3211390.24883347X-RAY DIFFRACTION100
3.69-3.820.3041450.24133379X-RAY DIFFRACTION100
3.82-3.970.28881400.24693422X-RAY DIFFRACTION99.94
3.97-4.160.25861460.2443376X-RAY DIFFRACTION99.97
4.16-4.370.29151450.23113400X-RAY DIFFRACTION99.97
4.37-4.650.24481430.19963409X-RAY DIFFRACTION99.92
4.65-5.010.20491430.18543367X-RAY DIFFRACTION99.97
5.01-5.510.21891410.21513446X-RAY DIFFRACTION99.89
5.51-6.310.23021390.23353448X-RAY DIFFRACTION100
6.31-7.940.24231490.23273438X-RAY DIFFRACTION99.39
7.94-48.860.20881420.17353556X-RAY DIFFRACTION98.9

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