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- PDB-2yic: Crystal structure of the SucA domain of Mycobacterium smegmatis a... -

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Basic information

Entry
Database: PDB / ID: 2yic
TitleCrystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase (triclinic form)
Components2-OXOGLUTARATE DECARBOXYLASE
KeywordsLYASE
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
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
THIAMINE DIPHOSPHATE / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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
DepositionMay 11, 2011Deposition 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
C: 2-OXOGLUTARATE DECARBOXYLASE
D: 2-OXOGLUTARATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,62516
Polymers388,6674
Non-polymers1,95912
Water21,9961221
1
A: 2-OXOGLUTARATE DECARBOXYLASE
B: 2-OXOGLUTARATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,3138
Polymers194,3332
Non-polymers9796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11130 Å2
ΔGint-91.1 kcal/mol
Surface area54550 Å2
MethodPISA
2
C: 2-OXOGLUTARATE DECARBOXYLASE
D: 2-OXOGLUTARATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,3138
Polymers194,3332
Non-polymers9796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-89 kcal/mol
Surface area54730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.539, 83.244, 158.610
Angle α, β, γ (deg.)99.48, 99.06, 101.25
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2153, 0.0659, 0.9743), (0.0662, -0.9944, 0.0819), (0.9743, 0.0822, 0.2097)45.5639, 4.6393, -37.083
2given(-0.925, -0.38, 0.0018), (-0.38, 0.925, 0.0008), (-0.002, 0.0001, -1)-0.3005, -0.0277, 0.5788
3given(0.1728, 0.1483, -0.9737), (0.3211, -0.9431, -0.0866), (-0.9311, -0.2977, -0.2106)46.1381, 4.9238, -37.0999

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Components

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


Mass: 97166.648 Da / Num. of mol.: 4 / Fragment: RESIDUES 361-1227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2155 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: A0R2B1, 2-oxoglutarate decarboxylase
#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#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.: 1221 / 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: 2.74 Å3/Da / Density % sol: 55.2 % / Description: NONE
Crystal growpH: 7 / Details: 46.5% MPD, 100 MM HEPES, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2009 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: CHANNEL CUT MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.96→49.5 Å / Num. obs: 263780 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 23.55 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.7
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 91.5

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XT9

2xt9
PDB Unreleased entry


Resolution: 1.96→39.2 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9108 / SU R Cruickshank DPI: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.148 / SU Rfree Blow DPI: 0.129 / SU Rfree Cruickshank DPI: 0.133
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=26355. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=MG CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=26355. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 13228 5.02 %RANDOM
Rwork0.1884 ---
obs0.1896 263738 95.19 %-
Displacement parametersBiso mean: 28.82 Å2
Baniso -1Baniso -2Baniso -3
1--2.9185 Å2-0.2784 Å21.1846 Å2
2--0.3211 Å20.8939 Å2
3---2.5975 Å2
Refine analyzeLuzzati coordinate error obs: 0.244 Å
Refinement stepCycle: LAST / Resolution: 1.96→39.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25015 0 112 1221 26348
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125646HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9834812HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11812SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes653HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3800HARMONIC5
X-RAY DIFFRACTIONt_it25646HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion2.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3331SEMIHARMONIC5
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_contact32085SEMIHARMONIC4
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2386 969 5.24 %
Rwork0.209 17538 -
all0.2105 18507 -
obs--95.19 %
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)
10.3882-0.15640.20990.5451-0.20640.6164-0.0076-0.03440.05530.0049-0.00170.10220.0256-0.03260.0093-0.07510.0319-0.0265-0.1022-0.0066-0.0579-4.81320.1412-32.3567
20.53360.13460.11820.75370.03690.49080.00060.06560.0222-0.1013-0.0137-0.06540.05270.08910.0131-0.10270.0508-0.0113-0.09390.0133-0.097615.30591.7099-48.3458
30.32350.01410.13950.61430.26690.6813-0.04440.01040.0851-0.0150.0298-0.0842-0.02080.01530.0146-0.07570.0216-0.0357-0.10180.0068-0.07454.08531.827832.829
40.6392-0.13820.12230.50570.00710.5538-0.0251-0.0938-0.00860.11410.00870.06890.066-0.14910.0164-0.09460.0161-0.0136-0.0712-0.0012-0.116-15.0268-4.545448.8379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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