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- PDB-6kma: Crystal structure of SucA with glycolaldehyde-1-13C from Vibrio v... -

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Basic information

Entry
Database: PDB / ID: 6kma
TitleCrystal structure of SucA with glycolaldehyde-1-13C from Vibrio vulnificus
ComponentsOxoglutarate dehydrogenase (Succinyl-transferring), E1 component
KeywordsOXIDOREDUCTASE / DEHYDROGENASE
Function / homology
Function and homology information


oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / glycolytic process / metal ion binding / cytosol
Similarity search - Function
2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / 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 ...2-oxoglutarate dehydrogenase E1 component, N-terminal domain / 2-oxoglutarate dehydrogenase N-terminus / 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-oxidanylethanal / THIAMINE DIPHOSPHATE / 2-oxoglutarate dehydrogenase E1 component
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.282 Å
AuthorsSeo, P.W. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: Catalysis Science And Technology / Year: 2020
Title: Understanding the molecular properties of the E1 subunit (SucA) of alpha-ketoglutarate dehydrogenase complex from Vibrio vulnificus for the enantioselective ligation of acetaldehydes into (R)-acetoin.
Authors: Seo, P.W. / Jo, H.J. / Hwang, I.Y. / Jeong, H.Y. / Kim, J.H. / Kim, J.W. / Lee, E.Y. / Park, J.B. / Kim, J.S.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
B: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
C: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
D: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,55226
Polymers398,0644
Non-polymers3,48822
Water22,3931243
1
A: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
B: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,77613
Polymers199,0322
Non-polymers1,74411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14260 Å2
ΔGint-41 kcal/mol
Surface area54680 Å2
MethodPISA
2
C: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
D: Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,77613
Polymers199,0322
Non-polymers1,74411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-39 kcal/mol
Surface area54810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.820, 84.559, 145.218
Angle α, β, γ (deg.)79.510, 88.470, 89.920
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 87 through 288 or resid 294 through 935))
21(chain B and (resid 87 through 288 or resid 294 through 935))
31(chain C and (resid 87 through 288 or resid 294 through 935))
41chain D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLYSLYS(chain A and (resid 87 through 288 or resid 294 through 935))AA87 - 28832 - 233
12GLYGLYVALVAL(chain A and (resid 87 through 288 or resid 294 through 935))AA294 - 935239 - 880
21ASPASPLYSLYS(chain B and (resid 87 through 288 or resid 294 through 935))BB87 - 28832 - 233
22GLYGLYVALVAL(chain B and (resid 87 through 288 or resid 294 through 935))BB294 - 935239 - 880
31ASPASPLYSLYS(chain C and (resid 87 through 288 or resid 294 through 935))CC87 - 28832 - 233
32GLYGLYVALVAL(chain C and (resid 87 through 288 or resid 294 through 935))CC294 - 935239 - 880
41ASPASPDW3DW3chain DDD - V87 - 100132

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Oxoglutarate dehydrogenase (Succinyl-transferring), E1 component


Mass: 99516.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (strain CMCP6) (bacteria)
Strain: CMCP6 / Gene: sucA, VV1_0157 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3Q0L1E1, oxoglutarate dehydrogenase (succinyl-transferring)

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Non-polymers , 6 types, 1265 molecules

#2: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-DW3 / 2-oxidanylethanal


Mass: 60.052 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1243 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 220 mM calcium acetate, 100mM 2-(Bis(2-hydroxyethyl)amino)acetic acid (BICINE), 50% (v/v) PEG300, 0.1 mM ThDP, 0.1 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 148472 / % possible obs: 91.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 32 Å2 / Rpim(I) all: 0.108 / Net I/σ(I): 6.2
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 7303 / Rpim(I) all: 0.53

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JGD

2jgd


Resolution: 2.282→47.648 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.52
RfactorNum. reflection% reflection
Rfree0.2299 5900 3.98 %
Rwork0.1997 --
obs0.2009 148359 90.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.81 Å2 / Biso mean: 37.1688 Å2 / Biso min: 16.22 Å2
Refinement stepCycle: final / Resolution: 2.282→47.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26464 0 218 1243 27925
Biso mean--41.05 36.86 -
Num. residues----3351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00227268
X-RAY DIFFRACTIONf_angle_d0.57536920
X-RAY DIFFRACTIONf_chiral_restr0.0433945
X-RAY DIFFRACTIONf_plane_restr0.0044871
X-RAY DIFFRACTIONf_dihedral_angle_d16.51916356
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A16422X-RAY DIFFRACTION10.234TORSIONAL
12B16422X-RAY DIFFRACTION10.234TORSIONAL
13C16422X-RAY DIFFRACTION10.234TORSIONAL
14D16422X-RAY DIFFRACTION10.234TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.282-2.3080.34361500.313377773
2.308-2.33510.32071980.2994478790
2.3351-2.36360.30882170.2767471892
2.3636-2.39350.28751810.2725477691
2.3935-2.4250.2912000.2617477691
2.425-2.45820.28012050.2594470491
2.4582-2.49330.31191900.2478476890
2.4933-2.53060.31651800.2471455488
2.5306-2.57010.28292020.2453440484
2.5701-2.61220.24832030.2338493795
2.6122-2.65730.28391870.2412505795
2.6573-2.70560.25992080.2411485194
2.7056-2.75760.24522060.2281489994
2.7576-2.81390.27462090.2247488193
2.8139-2.87510.29722040.2238480993
2.8751-2.9420.24272060.2151484392
2.942-3.01550.23831980.2087481191
3.0155-3.0970.22161760.2034454087
3.097-3.18810.24221930.2023455087
3.1881-3.2910.23281910.201491294
3.291-3.40860.22562020.1944493294
3.4086-3.54510.20352200.1865487093
3.5451-3.70630.19191990.1712490994
3.7063-3.90170.18482020.166473691
3.9017-4.1460.20441830.1651444485
4.146-4.46590.18511960.1532501996
4.4659-4.91490.17852120.153494995
4.9149-5.62510.22651930.1717484392
5.6251-7.08330.21141910.1956463989
7.0833-47.6480.20931980.1894476491
Refinement TLS params.Method: refined / Origin x: 23.7674 Å / Origin y: -28.0011 Å / Origin z: 71.6257 Å
111213212223313233
T0.167 Å2-0.0036 Å20.0256 Å2-0.1299 Å2-0.0119 Å2--0.1874 Å2
L0.2086 °2-0.0207 °20.0781 °2-0.0968 °2-0.0259 °2--0.1862 °2
S-0.023 Å °-0.0068 Å °-0.0115 Å °0.0062 Å °0.0268 Å °-0.0025 Å °-0.0136 Å °-0.0104 Å °-0.0023 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA86 - 1001
2X-RAY DIFFRACTION1allA1002 - 1003
3X-RAY DIFFRACTION1allB87 - 1001
4X-RAY DIFFRACTION1allB1002 - 1003
5X-RAY DIFFRACTION1allC86 - 1001
6X-RAY DIFFRACTION1allC1002 - 1003
7X-RAY DIFFRACTION1allD87 - 1001
8X-RAY DIFFRACTION1allD1002 - 1003
9X-RAY DIFFRACTION1allS1 - 1243

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