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- PDB-3zht: Crystal structure of the SucA domain of Mycobacterium smegmatis K... -

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Basic information

Entry
Database: PDB / ID: 3zht
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis KGD, first post-decarboxylation intermediate from 2-oxoadipate
ComponentsMULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
KeywordsOXIDOREDUCTASE / E1O
Function / homology
Function and homology information


2-hydroxy-3-oxoadipate synthase / 2-oxoglutarate decarboxylase / 2-oxoglutarate decarboxylase activity / 2-hydroxy-3-oxoadipate synthase activity / oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding
Similarity search - Function
TPP helical domain / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain / Rossmann fold - #12470 / 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 ...TPP helical domain / Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain / Rossmann fold - #12470 / 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 / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Chloramphenicol acetyltransferase-like domain superfamily / Thiamin diphosphate-binding fold / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-TD9 / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWagner, T. / Barilone, N. / Bellinzoni, M. / Alzari, P.M.
CitationJournal: Biochem.J. / Year: 2014
Title: A Dual Conformation of the Post-Decarboxylation Intermediate is Associated with Distinct Enzyme States in Mycobacterial Alpha-Ketoglutarate Decarboxylase (Kgd).
Authors: Wagner, T. / Barilone, N. / Alzari, P.M. / Bellinzoni, M.
History
DepositionDec 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
B: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
C: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
D: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,09016
Polymers388,6674
Non-polymers2,42312
Water19,6001088
1
A: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
B: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5458
Polymers194,3332
Non-polymers1,2126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint-52.5 kcal/mol
Surface area54880 Å2
MethodPISA
2
C: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
D: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,5458
Polymers194,3332
Non-polymers1,2126
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-48.5 kcal/mol
Surface area54820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.366, 83.800, 159.513
Angle α, β, γ (deg.)99.76, 99.06, 100.61
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1942, 0.06, 0.9791), (0.0621, -0.9954, 0.0733), (0.979, 0.0751, 0.1896)45.5568, 4.1429, -37.8003
2given(-0.9332, -0.3593, -0.0075), (-0.3593, 0.9332, -0.0006), (0.0072, 0.0021, -1)0.0852, 0.0655, 0.6261
3given(0.1652, 0.1323, -0.9773), (0.3053, -0.9491, -0.0769), (-0.9378, -0.2857, -0.1972)46.1252, 4.318, -37.5766

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Components

#1: Protein
MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME / 2-HYDROXY-3-OXOADIPATE SYNTHASE / HOA SYNTHASE / HOAS / 2-OXOGLUTARATE CARBOXY-LYASE / 2- ...2-HYDROXY-3-OXOADIPATE SYNTHASE / HOA SYNTHASE / HOAS / 2-OXOGLUTARATE CARBOXY-LYASE / 2-OXOGLUTARATE DECARBOXYLASE / ALPHA-KETOGLUTARATE DECARBOXYLASE / KG DECARBOXYLASE / KGD / ALPHA-KETOGLUTARATE-GLYOXYLATE CARBOLIGASE / 2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT / ODH E1 COMPONENT / ALPHA-KETOGLUTARATE DEHYDROGENASE E1 COMPONENT / KDH E1 COMPONENT / DIHYDROLIPOYLLYSINE-RESIDUE SUCCINYLTRANSFERASE COMPONENT OF 2-OXOGLUTARATE DEHYDROGENASE COMPLEX / 2-OXOGLUTARATE DEHYDROGENASE COMPLEX E2 COMPONENT / ODH E2 COMPONENT / OGDC-E2 / DIHYDROLIPOAMIDE SUCCINYLTRANSFERASE


Mass: 97166.648 Da / Num. of mol.: 4 / Fragment: SUCA-LIKE CATALYTIC DOMAIN, RESIDUES 361-1127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2_155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: A0R2B1, 2-hydroxy-3-oxoadipate synthase, 2-oxoglutarate decarboxylase, oxoglutarate dehydrogenase (succinyl-transferring), dihydrolipoyllysine-residue succinyltransferase
#2: Chemical
ChemComp-TD9 / (5S)-5-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-5-(2-{[(phosphonatooxy)phosphinato]oxy}ethyl)-1,3-thiazol-3-ium-2-yl}-5-hydroxypentanoate


Mass: 541.430 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N4O10P2S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1088 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TER FIRST GLYCINE RESIDUE IS A PURIFICATION TAG LEFTOVER (TEV CLEAVAGE SITE)

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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: 2.63 Å3/Da / Density % sol: 53.3 % / Description: NONE
Crystal growpH: 7 / Details: 59% MPD, 22.5 MM NA ACETATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: SI(111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.15→41.82 Å / Num. obs: 209671 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 39.66 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 96.5

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YIC

2yic


Resolution: 2.15→41.11 Å / Cor.coef. Fo:Fc: 0.9218 / Cor.coef. Fo:Fc free: 0.9082 / SU R Cruickshank DPI: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.232 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.188
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 10531 5.02 %RANDOM
Rwork0.223 ---
obs0.2241 209661 97.49 %-
Displacement parametersBiso mean: 43.94 Å2
Baniso -1Baniso -2Baniso -3
1--3.1108 Å21.9324 Å2-1.5589 Å2
2---0.0366 Å20.2256 Å2
3---3.1474 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.15→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24960 0 144 1088 26192
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125620HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0134781HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11790SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes651HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3862HARMONIC5
X-RAY DIFFRACTIONt_it25620HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion2.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3328SEMIHARMONIC5
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_contact31365SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2535 794 5.18 %
Rwork0.2234 14520 -
all0.225 15314 -
obs--97.49 %
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)
10.6418-0.33280.16141.0479-0.4861.1395-0.03910.06190.1616-0.0430.0870.2666-0.0987-0.1188-0.048-0.1540.1037-0.0464-0.11970.07670.0212-16.572315.2267-45.564
20.6277-0.12160.1650.6284-0.21290.8548-0.0295-0.0803-0.06780.12650.06150.06990.1480.0628-0.0321-0.00730.16610.0303-0.08060.0356-0.09256.5821-15.4449-19.4726
31.10620.02890.25860.95230.02550.4855-0.00830.3213-0.1654-0.2430.03170.07360.18960.1498-0.0234-0.01690.093-0.0151-0.0255-0.0305-0.16145.3614-15.243-61.378
41.00780.15530.01471.0527-0.35910.5266-0.06910.00980.27870.06810.0245-0.2156-0.11220.15480.0446-0.14310.0786-0.0354-0.07130.0112-0.019524.137218.5221-36.2774
50.5608-0.01510.12791.07670.21880.9106-0.1161-0.12080.29540.02370.0712-0.2263-0.18160.06980.0449-0.0870.0872-0.0854-0.1559-0.05240.0429.658820.18746.2276
60.61540.0210.08160.73160.19690.9273-0.00490.0614-0.0371-0.22270.0099-0.08490.131-0.007-0.0050.03930.06980.0318-0.13660.0217-0.0998-0.54-16.853620.1391
71.2156-0.22190.20870.8672-0.16630.5577-0.0592-0.3545-0.13040.12940.0396-0.08580.1217-0.09510.0196-0.07210.1306-0.0179-0.00460.0745-0.14820.0221-16.512161.8151
81.0808-0.371-0.03961.13920.0710.7099-0.0768-0.10080.0774-0.07560.06060.2762-0.0776-0.230.0161-0.14340.1179-0.0626-0.05760.0216-0.0552-29.37578.372536.6443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 366-810
2X-RAY DIFFRACTION2CHAIN A AND RESID 831-1227
3X-RAY DIFFRACTION3CHAIN B AND RESID 365-810
4X-RAY DIFFRACTION4CHAIN B AND RESID 831-1227
5X-RAY DIFFRACTION5CHAIN C AND RESID 367-810
6X-RAY DIFFRACTION6CHAIN C AND RESID 831-1227
7X-RAY DIFFRACTION7CHAIN D AND RESID 367-810
8X-RAY DIFFRACTION8CHAIN D AND RESID 831-1227

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