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- PDB-2xt6: Crystal structure of Mycobacterium smegmatis alpha-ketoglutarate ... -

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Basic information

Entry
Database: PDB / ID: 2xt6
TitleCrystal structure of Mycobacterium smegmatis alpha-ketoglutarate decarboxylase homodimer (orthorhombic form)
Components2-OXOGLUTARATE DECARBOXYLASE
KeywordsLYASE / KDH / KGD
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 / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding ...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 / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / magnesium ion binding / cytosol
Similarity search - Function
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 ...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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsWagner, T. / Bellinzoni, M. / Wehenkel, A.M. / O'Hare, H.M. / Alzari, P.M.
CitationJournal: Chem.Biol. / Year: 2011
Title: Functional Plasticity and Allosteric Regulation of Alpha-Ketoglutarate Decarboxylase in Central Mycobacterial Metabolism.
Authors: Wagner, T. / Bellinzoni, M. / Wehenkel, A.M. / O'Hare, H.M. / Alzari, P.M.
History
DepositionOct 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references / Version format compliance
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: 2-OXOGLUTARATE DECARBOXYLASE
B: 2-OXOGLUTARATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,1728
Polymers248,1932
Non-polymers9796
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-86.1 kcal/mol
Surface area72570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.990, 247.720, 79.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9623, -0.2124, -0.1697), (-0.2111, 0.19, 0.9588), (-0.1714, 0.9585, -0.2277)
Vector: 31.9976, 63.7241, -72.1522)

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Components

#1: Protein 2-OXOGLUTARATE DECARBOXYLASE / ALPHA-KETOGLUTARATE DECARBOXYLASE / 2-OXOGLUTARATE CARBOXY-LYASE


Mass: 124096.305 Da / Num. of mol.: 2 / Fragment: RESIDUES 116-1227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: A0R2B1, 2-oxoglutarate decarboxylase
#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.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST GLY 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: 3.3 Å3/Da / Density % sol: 62.7 % / Description: NONE
Crystal growpH: 7 / Details: 39% MPD, 100 MM HEPES, PH 7.0, 200 MM NACL

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0332
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 26, 2009 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.74→82 Å / Num. obs: 79835 / % possible obs: 99.3 % / Observed criterion σ(I): 2.4 / Redundancy: 3.5 % / Biso Wilson estimate: 75.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.3
Reflection shellResolution: 2.74→2.89 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / % possible all: 97.5

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Processing

Software
NameVersionClassification
BUSTER-TNT2.9.3refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XT9

2xt9
PDB Unreleased entry


Resolution: 2.74→40.12 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.8741 / SU R Cruickshank DPI: 0.508 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.48 / SU Rfree Blow DPI: 0.267 / SU Rfree Cruickshank DPI: 0.274
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 4017 5.05 %RANDOM
Rwork0.1854 ---
obs0.1874 79534 99.13 %-
Displacement parametersBiso mean: 70.04 Å2
Baniso -1Baniso -2Baniso -3
1-25.4159 Å20 Å20 Å2
2---9.113 Å20 Å2
3----16.303 Å2
Refine analyzeLuzzati coordinate error obs: 0.377 Å
Refinement stepCycle: LAST / Resolution: 2.74→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15727 0 56 119 15902
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116094HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0921842HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7384SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes401HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2392HARMONIC5
X-RAY DIFFRACTIONt_it16040HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion2.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2110SEMIHARMONIC5
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_contact18651SEMIHARMONIC4
LS refinement shellResolution: 2.74→2.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2937 294 5.23 %
Rwork0.2332 5324 -
all0.2364 5618 -
obs--99.13 %
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)
17.16020.0757-0.50331.30390.11350.238-0.08520.1840.8317-0.009-0.04710.1060.0836-0.11410.1323-0.06040.02720.0257-0.0887-0.05860.3696-40.192103.20621.998
21.0146-0.2429-0.29470.48870.35660.6818-0.01860.16930.4615-0.1252-0.00290.2284-0.1524-0.16690.0215-0.0479-0.0018-0.06280.0020.17570.0795-9.243289.5636-3.9736
31.59730.2896-0.17131.18460.1090.8994-0.08070.4002-0.1695-0.27030.1487-0.0817-0.09860.1372-0.0679-0.0754-0.1011-0.03180.07060.0341-0.310927.314266.4144-25.004
45.23032.1927-0.47672.10271.50341.6177-0.1921-0.54082.35070.14190.3085-0.74640.34790.0957-0.1164-0.34520.1321-0.3261-0.2474-0.23161.206941.3218109.33328.6535
52.41320.64570.64051.37550.29370.39010.0005-0.20580.20820.19860.0035-0.0007-0.0153-0.0679-0.004-0.0547-0.0501-0.01120.02450.0946-0.266522.214579.551616.3575
61.27890.1897-0.15460.63420.11630.60550.00820.038-0.52930.0435-0.02530.16520.0581-0.11550.0171-0.1148-0.0817-0.0654-0.07760.09770.0213-4.26246.6851-7.3845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A121 - A347)
2X-RAY DIFFRACTION2(A348 - A814)
3X-RAY DIFFRACTION3(A831 - A2003)
4X-RAY DIFFRACTION4(B128 - B347)
5X-RAY DIFFRACTION5(B348 - B810)
6X-RAY DIFFRACTION6(B832 - B2003)

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