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- PDB-9vkn: Crystal structure of DhdR in complex with inducer L2HG -

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Basic information

Entry
Database: PDB / ID: 9vkn
TitleCrystal structure of DhdR in complex with inducer L2HG
ComponentsPyruvate 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
(2S)-2-HYDROXYPENTANEDIOIC ACID / Pyruvate dehydrogenase complex repressor
Similarity search - Component
Biological speciesAchromobacter denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 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
DepositionJun 23, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: 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

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Assembly

Deposited unit
A: Pyruvate dehydrogenase complex repressor
B: Pyruvate dehydrogenase complex repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3738
Polymers32,8752
Non-polymers4986
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-32 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.984, 126.984, 39.776
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Pyruvate dehydrogenase complex repressor / DhdR


Mass: 16437.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Achromobacter denitrificans (bacteria) / Gene: FOC81_30220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N0JVZ6
#2: Chemical ChemComp-S2G / (2S)-2-HYDROXYPENTANEDIOIC ACID


Mass: 148.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1.8 M Ammonium phosphate monobasic; 0.1 M Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.24→90.18 Å / Num. obs: 16262 / % possible obs: 99.1 % / Redundancy: 20 % / Biso Wilson estimate: 35.62 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.019 / Rrim(I) all: 0.089 / Χ2: 1.05 / Net I/σ(I): 28.7
Reflection shellResolution: 2.24→2.37 Å / % possible obs: 94 % / Redundancy: 13 % / Rmerge(I) obs: 0.677 / Num. measured all: 28584 / Num. unique obs: 2200 / CC1/2: 0.929 / Rpim(I) all: 0.197 / Rrim(I) all: 0.707 / Χ2: 0.84 / Net I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→24.81 Å / SU ML: 0.2154 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.2142 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2396 639 5.04 %
Rwork0.1981 12035 -
obs0.2003 12674 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.26 Å2
Refinement stepCycle: LAST / Resolution: 2.44→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 24 28 2206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812199
X-RAY DIFFRACTIONf_angle_d0.97682991
X-RAY DIFFRACTIONf_chiral_restr0.0499357
X-RAY DIFFRACTIONf_plane_restr0.0062400
X-RAY DIFFRACTIONf_dihedral_angle_d24.4299769
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.620.26131230.21852352X-RAY DIFFRACTION99.6
2.62-2.890.27411060.23552386X-RAY DIFFRACTION100
2.89-3.30.31331290.23632370X-RAY DIFFRACTION99.96
3.3-4.160.22591380.18732390X-RAY DIFFRACTION99.37
4.16-24.810.21811430.1812537X-RAY DIFFRACTION99.81

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