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- PDB-9jpl: Crystal structure of DhdR inducer binding domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9jpl
TitleCrystal structure of DhdR inducer binding domain in complex with inducer
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
(2R)-2-hydroxypentanedioic acid / Pyruvate dehydrogenase complex repressor
Similarity search - Component
Biological speciesAchromobacter denitrificans NBRC 15125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 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)51,7868
Polymers51,1762
Non-polymers6116
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-19 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.000, 128.000, 42.950
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
Components on special symmetry positions
IDModelComponents
11A-452-

HOH

21A-453-

HOH

31A-467-

HOH

41B-436-

HOH

51B-451-

HOH

61B-453-

HOH

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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 NBRC 15125 (bacteria)
Gene: FOC81_30220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N0JVZ6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-2HG / (2R)-2-hydroxypentanedioic acid


Mass: 148.114 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H8O5
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 120 / 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: 0.1 M Bis Tris, pH 5.5, 25% w/v PEG 3350

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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: 2.01→50 Å / Num. obs: 24439 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 35.82 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.3
Reflection shellResolution: 2.01→10 Å / Num. unique obs: 24439 / CC1/2: 0.654

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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: 2.01→40.72 Å / SU ML: 0.2186 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.3274 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2297 1196 4.9 %
Rwork0.2002 23195 -
obs0.2017 24391 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.74 Å2
Refinement stepCycle: LAST / Resolution: 2.01→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 33 120 2377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072278
X-RAY DIFFRACTIONf_angle_d0.87493090
X-RAY DIFFRACTIONf_chiral_restr0.0444363
X-RAY DIFFRACTIONf_plane_restr0.005415
X-RAY DIFFRACTIONf_dihedral_angle_d13.30181382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.090.31741270.25022533X-RAY DIFFRACTION100
2.09-2.190.26541200.21952532X-RAY DIFFRACTION100
2.19-2.30.29541580.21182517X-RAY DIFFRACTION100
2.3-2.440.20651140.19532548X-RAY DIFFRACTION100
2.44-2.630.26151330.20412543X-RAY DIFFRACTION100
2.63-2.90.26561320.2092566X-RAY DIFFRACTION100
2.9-3.320.27631320.20832587X-RAY DIFFRACTION100
3.32-4.180.18821480.18942594X-RAY DIFFRACTION100
4.18-40.720.20981320.1922775X-RAY DIFFRACTION99.86

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