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- PDB-9jpj: Crystal structure of DhdR in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 9jpj
TitleCrystal structure of DhdR in complex with DNA
Components
  • (DNA (27-MER)) x 2
  • Pyruvate dehydrogenase complex repressor
KeywordsTRANSCRIPTION / Transcriptional regulator
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Pyruvate dehydrogenase complex repressor
Similarity search - Component
Biological speciesAchromobacter denitrificans NBRC 15125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.72 Å
AuthorsSun, P. / Wang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Chem Biol / Year: 2025
Title: Development of D2HG biosensors inspired by the molecular mechanism of D2HG regulation of DhdR.
Authors: Wang, B. / Luo, S. / Sun, P.
History
DepositionSep 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: DNA (27-MER)
H: DNA (27-MER)
C: Pyruvate dehydrogenase complex repressor
D: Pyruvate dehydrogenase complex repressor
A: DNA (27-MER)
B: DNA (27-MER)
E: Pyruvate dehydrogenase complex repressor
F: Pyruvate dehydrogenase complex repressor
I: Pyruvate dehydrogenase complex repressor
J: Pyruvate dehydrogenase complex repressor
K: Pyruvate dehydrogenase complex repressor
L: Pyruvate dehydrogenase complex repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,40120
Polymers237,87812
Non-polymers5238
Water00
1
G: DNA (27-MER)
H: DNA (27-MER)
I: Pyruvate dehydrogenase complex repressor
J: Pyruvate dehydrogenase complex repressor
K: Pyruvate dehydrogenase complex repressor
L: Pyruvate dehydrogenase complex repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,20110
Polymers118,9396
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18540 Å2
ΔGint-227 kcal/mol
Surface area46010 Å2
MethodPISA
2
C: Pyruvate dehydrogenase complex repressor
D: Pyruvate dehydrogenase complex repressor
A: DNA (27-MER)
B: DNA (27-MER)
E: Pyruvate dehydrogenase complex repressor
F: Pyruvate dehydrogenase complex repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,20110
Polymers118,9396
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17570 Å2
ΔGint-222 kcal/mol
Surface area48590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.456, 87.044, 133.884
Angle α, β, γ (deg.)91.480, 102.480, 117.550
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: DNA chain DNA (27-MER)


Mass: 8365.462 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter denitrificans NBRC 15125 (bacteria)
Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (27-MER)


Mass: 8222.315 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter denitrificans NBRC 15125 (bacteria)
Production host: Escherichia coli (E. coli)
#3: Protein
Pyruvate dehydrogenase complex repressor / DhdR


Mass: 25587.777 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter denitrificans NBRC 15125 (bacteria)
Gene: FOC81_30220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N0JVZ6
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
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: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammonium sulfate, 0.1 M Tris hydrochloride pH 8.5

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Data collection

DiffractionMean temperature: 177 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979145 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979145 Å / Relative weight: 1
ReflectionResolution: 3.72→50 Å / Num. obs: 30547 / % possible obs: 95.5 % / Redundancy: 4.5 % / CC1/2: 1 / Net I/σ(I): 12.31
Reflection shellResolution: 3.72→50 Å / Num. unique obs: 30388 / CC1/2: 0.885

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 3.72→39.26 Å / SU ML: 0.5917 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 37.0682 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2986 1471 4.84 %
Rwork0.2501 28917 -
obs0.2526 30388 93.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 159.36 Å2
Refinement stepCycle: LAST / Resolution: 3.72→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12121 2210 8 0 14339

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