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

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Basic information

Entry
Database: PDB / ID: 5rvw
TitlePanDDA analysis group deposition -- Crystal Structure of DHTKD1 in complex with Z1587220559
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
2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol / THIAMINE DIPHOSPHATE / 2-oxoadipate dehydrogenase complex component E1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.614 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)203,0158
Polymers201,8522
Non-polymers1,1636
Water32,4631802
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-65 kcal/mol
Surface area54840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.074, 147.025, 87.377
Angle α, β, γ (deg.)90.000, 102.700, 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: Chemical ChemComp-T1J / 2-{[(1H-benzimidazol-2-yl)amino]methyl}phenol


Mass: 239.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N3O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1802 / 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: 49.25 % / 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 6M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9126 Å / Relative weight: 1
ReflectionResolution: 1.614→85.24 Å / Num. obs: 136689 / % possible obs: 94.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.46 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.058 / Rrim(I) all: 0.115 / Net I/σ(I): 8.7 / Num. measured all: 521455 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.614-1.8223.42339368350.6550.4260.8091.767.7
5.356-85.243.8258530.9990.0210.04224.799.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (20-MAY-2020)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6SY1

6sy1


Resolution: 1.614→85.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 6725 4.92 %RANDOM
Rwork0.1635 ---
obs0.1647 136691 55.6 %-
Displacement parametersBiso max: 123.12 Å2 / Biso mean: 25.51 Å2 / Biso min: 6.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.7339 Å20 Å20.5961 Å2
2---0.3425 Å20 Å2
3---2.0765 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.614→85.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13480 0 73 1802 15355
Biso mean--17.66 34.92 -
Num. residues----1734
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4755SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2375HARMONIC5
X-RAY DIFFRACTIONt_it13933HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1777SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15251SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13933HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg18923HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion3.68
X-RAY DIFFRACTIONt_other_torsion15.96
LS refinement shellResolution: 1.61→1.76 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2654 120 4.39 %
Rwork0.2213 2614 -
all-2734 -
obs--4.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3142-0.0244-0.02980.18280.18870.2996-0.0024-0.02780.0401-0.04870.0154-0.0542-0.0010.0382-0.0129-0.0545-0.0010.0138-0.04670.00190.043510.662314.6816-36.1071
20.44-0.0489-0.04430.12270.16240.3094-0.0282-0.1061-0.05370.0356-0.03010.0860.1024-0.07040.0583-0.0541-0.00920.0335-0.04120.03120.0414-9.55553.0623-24.2661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A53 - 919
2X-RAY DIFFRACTION2{ B|* }B49 - 919

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