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- PDB-5rw1: PanDDA analysis group deposition of ground-state model of DHTKD1 -

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Basic information

Entry
Database: PDB / ID: 5rw1
TitlePanDDA analysis group deposition of ground-state model of DHTKD1
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 / 2-oxoadipate dehydrogenase activity / OADH complex synthesizes glutaryl-CoA from 2-OA / oxoadipate dehydrogenase complex / oxoglutarate dehydrogenase (succinyl-transferring) activity / thiamine pyrophosphate binding / hematopoietic progenitor cell differentiation / glycolytic process / generation of precursor metabolites and energy / mitochondrial matrix / mitochondrion
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 / 2-oxoadipate dehydrogenase complex component E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.52 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 of ground-state model
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

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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)202,7767
Polymers201,8522
Non-polymers9245
Water32,6251811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12430 Å2
ΔGint-64 kcal/mol
Surface area54870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.139, 147.337, 87.637
Angle α, β, γ (deg.)90.000, 102.780, 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-TPP / THIAMINE DIPHOSPHATE


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


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


Mass: 18.015 Da / Num. of mol.: 1811 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.53 % / Mosaicity: 0.09 °
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 2M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9126 Å / Relative weight: 1
ReflectionResolution: 1.56→64.39 Å / Num. obs: 273569 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.043 / Rrim(I) all: 0.082 / Net I/σ(I): 9.2 / Num. measured all: 881493 / Scaling rejects: 72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.56-1.642.21.2485387395850.40.9581.5770.698.4
4.92-64.393.90.0263421388520.9990.0160.03137.899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0266refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6SY1

6sy1


Resolution: 1.52→64.48 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.696 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 10093 4.9 %RANDOM
Rwork0.1641 ---
obs0.1654 194125 68.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.88 Å2 / Biso mean: 18.703 Å2 / Biso min: 5.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.04 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.52→64.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13505 0 55 1811 15371
Biso mean--9.42 30.87 -
Num. residues----1732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01313936
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712993
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.6418916
X-RAY DIFFRACTIONr_angle_other_deg1.4841.57229957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27351741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1822.288708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02152308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.681578
X-RAY DIFFRACTIONr_chiral_restr0.0850.21778
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023174
X-RAY DIFFRACTIONr_mcbond_it1.9031.8236937
X-RAY DIFFRACTIONr_mcbond_other1.9021.8236936
X-RAY DIFFRACTIONr_mcangle_it2.932.7278666
LS refinement shellResolution: 1.516→1.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 39 -
Rwork0.266 840 -
all-879 -
obs--3.99 %

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