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- PDB-9jpk: Crystal structure of DhdR inducer binding domain -

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Basic information

Entry
Database: PDB / ID: 9jpk
TitleCrystal structure of DhdR inducer binding domain
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
Pyruvate dehydrogenase complex repressor
Similarity search - Component
Biological speciesAchromobacter denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsSun, P. / Wang, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of DhdR inducer binding domain
Authors: Sun, P. / Wang, B.
History
DepositionSep 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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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)51,3064
Polymers51,1762
Non-polymers1312
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-79 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.745, 64.641, 65.432
Angle α, β, γ (deg.)90.000, 124.207, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Pyruvate dehydrogenase complex repressor / DhdR


Mass: 25587.777 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium chloride, 20% w/v Polyethylene glycol 3,350, pH 7.0

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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 PILATUS3 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: 2.28→50 Å / Num. obs: 14804 / % possible obs: 98.5 % / Redundancy: 3 % / Biso Wilson estimate: 27.56 Å2 / CC1/2: 0.895 / Net I/σ(I): 6.2
Reflection shellResolution: 2.28→10 Å / Num. unique obs: 14840 / CC1/2: 0.883

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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: 2.28→31.39 Å / SU ML: 0.2965 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8243 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2706 741 5.01 %
Rwork0.2308 14063 -
obs0.2327 14804 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.8 Å2
Refinement stepCycle: LAST / Resolution: 2.28→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 2 115 2248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02572159
X-RAY DIFFRACTIONf_angle_d2.23392938
X-RAY DIFFRACTIONf_chiral_restr0.1692348
X-RAY DIFFRACTIONf_plane_restr0.013393
X-RAY DIFFRACTIONf_dihedral_angle_d28.692758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.460.39051390.28462752X-RAY DIFFRACTION98.77
2.46-2.70.26621360.26452834X-RAY DIFFRACTION99.87
2.7-3.090.29281610.25892784X-RAY DIFFRACTION100
3.09-3.90.26861530.22622816X-RAY DIFFRACTION99.56
3.9-31.390.22811520.19642877X-RAY DIFFRACTION99.8

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