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- PDB-5rvz: PanDDA analysis group deposition -- Crystal Structure of DHTKD1 i... -

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Basic information

Entry
Database: PDB / ID: 5rvz
TitlePanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z1929757385
ComponentsProbable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial
KeywordsOXIDOREDUCTASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With a disulfide as acceptor / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / Glyoxylate metabolism and glycine degradation / thiamine pyrophosphate binding / hematopoietic progenitor cell differentiation / tricarboxylic acid cycle / generation of precursor metabolites and energy / glycolytic process / mitochondrial matrix ...Oxidoreductases; Acting on the aldehyde or oxo group of donors; With a disulfide as acceptor / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / Glyoxylate metabolism and glycine degradation / thiamine pyrophosphate binding / hematopoietic progenitor cell differentiation / tricarboxylic acid cycle / generation of precursor metabolites and energy / glycolytic process / mitochondrial matrix / mitochondrion / cytosol
Similarity search - Function
Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily / 2-oxoglutarate dehydrogenase C-terminal / 2-oxoglutarate dehydrogenase E1 component / Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Chem-WGA / 2-oxoadipate dehydrogenase complex component E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.98 Å
AuthorsBezerra, G.A. / Foster, W.R. / Bailey, H.J. / Shrestha, L. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. ...Bezerra, G.A. / Foster, W.R. / Bailey, H.J. / Shrestha, L. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W.W.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Bezerra, G.A. / Foster, W.R. / Bailey, H.J. / Shrestha, L. / Krojer, T. / Brandao-Neto, J. / Douangamath, A. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W.W.
History
DepositionOct 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial
B: Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,9868
Polymers201,8522
Non-polymers1,1346
Water32,5891809
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12450 Å2
ΔGint-65 kcal/mol
Surface area54330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.149, 146.911, 87.327
Angle α, β, γ (deg.)90.000, 102.900, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable 2-oxoglutarate dehydrogenase E1 component DHKTD1, mitochondrial / Dehydrogenase E1 and transketolase domain-containing protein 1


Mass: 100926.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHTKD1, KIAA1630 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96HY7, oxoglutarate dehydrogenase (succinyl-transferring)
#2: Chemical ChemComp-WGA / (3S)-1-(3-fluoropyridin-2-yl)-4,4-dimethylpyrrolidin-3-ol


Mass: 210.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15FN2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1809 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.19 % / Mosaicity: 0.28 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.1M Hepes, 0.1M Magnesium chloride, 20% PEG 6K, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9126 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9126 Å / Relative weight: 1
ReflectionResolution: 1.989→85.122 Å / Num. obs: 78185 / % possible obs: 92.4 % / Redundancy: 3.7 % / CC1/2: 0.99 / Rpim(I) all: 0.097 / Rrim(I) all: 0.188 / Net I/σ(I): 6.9 / Num. measured all: 291693 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 %

Resolution (Å)Num. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.989-2.2421414039090.5550.4770.9121.666.3
6.437-85.122139760.9980.0250.04819.998.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6SY1

6sy1


Resolution: 1.98→85.12 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.203 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.439 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 3950 5.1 %RANDOM
Rwork0.1657 ---
obs0.1688 74266 58.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.05 Å2 / Biso mean: 24.78 Å2 / Biso min: 3.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20.19 Å2
2---0.01 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.98→85.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13480 0 70 1809 15359
Biso mean--17.14 32.48 -
Num. residues----1734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01313929
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712668
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.64118920
X-RAY DIFFRACTIONr_angle_other_deg1.2961.56929428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55651745
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49322.382701
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.943152283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8081575
X-RAY DIFFRACTIONr_chiral_restr0.0660.21780
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022886
X-RAY DIFFRACTIONr_mcbond_it2.0182.6076947
X-RAY DIFFRACTIONr_mcbond_other2.0172.6076946
X-RAY DIFFRACTIONr_mcangle_it3.2613.9068682
LS refinement shellResolution: 1.976→2.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 14 -
Rwork0.261 172 -
all-186 -
obs--1.87 %

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