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- PDB-3zhq: Crystal structure of the H747A mutant of the SucA domain of Mycob... -

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Basic information

Entry
Database: PDB / ID: 3zhq
TitleCrystal structure of the H747A mutant of the SucA domain of Mycobacterium smegmatis KGD
ComponentsMULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
KeywordsOXIDOREDUCTASE / E1O / THIAMINE DIPHOSPHATE
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
THIAMINE DIPHOSPHATE / Multifunctional 2-oxoglutarate metabolism enzyme
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 22, 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)390,35716
Polymers388,3984
Non-polymers1,95912
Water11,584643
1
A: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
B: MULTIFUNCTIONAL 2-OXOGLUTARATE METABOLISM ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,1798
Polymers194,1992
Non-polymers9796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint-87.1 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)195,1798
Polymers194,1992
Non-polymers9796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11090 Å2
ΔGint-86.1 kcal/mol
Surface area55150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.675, 83.737, 159.577
Angle α, β, γ (deg.)99.86, 98.95, 100.44
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.187, 0.0616, 0.9804), (0.0623, -0.9953, 0.0744), (0.9804, 0.075, 0.1822)45.547, 4.2491, -38.0905
2given(-0.9354, -0.3533, -0.011), (-0.3533, 0.9355, -0.0015), (0.0108, 0.0025, -0.9999)0.2265, 0.1867, 0.6519
3given(0.161, 0.1301, -0.9783), (0.2982, -0.9513, -0.0775), (-0.9408, -0.2793, -0.192)46.1597, 4.2935, -37.7432

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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: 97099.586 Da / Num. of mol.: 4 / Fragment: SUCA-LIKE CATALYTIC DOMAIN, RESIDUES 361-1227 / Mutation: YES
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-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


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 / Water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 2.65 Å3/Da / Density % sol: 53.5 % / Description: NONE
Crystal growpH: 7.6 / Details: 52% MPD, 20 MM NA ACETATE, pH 7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9535
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2011 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(311) - SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 2.5→48.97 Å / Num. obs: 133094 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 51.91 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.1
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 94.4

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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: 2.5→48.97 Å / Cor.coef. Fo:Fc: 0.8811 / Cor.coef. Fo:Fc free: 0.8607 / SU R Cruickshank DPI: 0.454 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.409 / SU Rfree Blow DPI: 0.239 / SU Rfree Cruickshank DPI: 0.248
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=25773. 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=25773. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 6716 5.05 %RANDOM
Rwork0.1937 ---
obs0.1952 133022 96.85 %-
Displacement parametersBiso mean: 43.94 Å2
Baniso -1Baniso -2Baniso -3
1--16.2664 Å2-5.3248 Å26.8032 Å2
2--6.7071 Å26.7995 Å2
3---9.5593 Å2
Refine analyzeLuzzati coordinate error obs: 0.326 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25015 0 112 643 25770
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0125641HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0534803HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11804SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes648HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3797HARMONIC5
X-RAY DIFFRACTIONt_it25641HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion2.75
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3330SEMIHARMONIC5
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_contact30740SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2686 498 5.15 %
Rwork0.2193 9176 -
all0.2219 9674 -
obs--96.85 %
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)
10.7993-0.23520.15911.2977-0.16850.7380.01740.08160.1376-0.00720.02450.23-0.0227-0.0723-0.0419-0.2598-0.00540.0531-0.06730.05490.0742-16.748415.2438-45.7194
20.6578-0.11360.10360.8269-0.05430.74660.0005-0.0801-0.06210.23250.04040.04430.220.0828-0.041-0.04070.06750.0541-0.08620.0412-0.06296.4682-15.2546-19.7081
31.1286-0.0217-0.01941.08860.06850.70230.04070.3219-0.1722-0.21380.01490.02650.23190.1025-0.0556-0.13410.0345-0.0006-0.006-0.0318-0.08865.1907-15.3723-61.436
40.76610.0378-0.0541.0659-0.26130.6573-0.03080.02270.19060.150.0337-0.2643-0.09040.2025-0.0029-0.2622-0.01110.0265-0.00540.00360.051624.106818.4001-36.4964
50.6175-0.17420.12171.35050.03210.8838-0.0565-0.09570.2076-0.09580.0536-0.2872-0.18010.04870.0029-0.1564-0.04180.0508-0.1115-0.00910.0349.965820.033846.3947
60.5535-0.08970.09880.95790.28210.69150.03250.0606-0.0103-0.36830.0087-0.11680.1093-0.0164-0.04120.0623-0.03760.0897-0.13340.049-0.1222-0.5677-16.760920.2755
71.0507-0.2564-0.10760.8689-0.17160.7751-0.0634-0.275-0.09650.09280.0767-0.04840.1429-0.0591-0.0133-0.1651-0.02860.0440.00290.0989-0.08230.4114-16.478962.1495
81.0036-0.3028-0.09240.89650.14870.83990.01530.00710.0533-0.1912-0.0010.2552-0.0758-0.2939-0.0143-0.1725-0.01670.0006-0.01420.0872-0.0539-29.11348.474836.9128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 366-810
2X-RAY DIFFRACTION2CHAIN A AND RESID 833-1227
3X-RAY DIFFRACTION3CHAIN B AND RESID 365-810
4X-RAY DIFFRACTION4CHAIN B AND RESID 833-1227
5X-RAY DIFFRACTION5CHAIN C AND RESID 368-810
6X-RAY DIFFRACTION6CHAIN C AND RESID 833-1227
7X-RAY DIFFRACTION7CHAIN D AND RESID 367-810
8X-RAY DIFFRACTION8CHAIN D AND RESID 833-1227 }

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