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- PDB-3l60: Crystal structure of branched-chain alpha-keto acid dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 3l60
TitleCrystal structure of branched-chain alpha-keto acid dehydrogenase subunit e2 from mycobacterium tuberculosis
ComponentsBRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI-2 / DEHYDROGENASE / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC
Function / homology
Function and homology information


dihydrolipoyllysine-residue (2-methylpropanoyl)transferase / dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity / lipoic acid binding / acetyltransferase activity / peptidoglycan-based cell wall / plasma membrane / cytoplasm
Similarity search - Function
Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. ...Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Dihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZencheck, W.D. / Bonanno, J.B. / Patskovsky, Y. / Toro, R. / Freeman, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Branched-Chain Alpha-Keto Acid Dehydrogenase Subunit E2 from Mycobacterium Tuberculosis
Authors: Zencheck, W.D. / Bonanno, J.B. / Patskovsky, Y. / Toro, R. / Freeman, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionDec 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2016Group: Structure summary
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)26,6762
Polymers26,6761
Non-polymers01
Water2,522140
1
A: BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE

A: BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE

A: BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)80,0276
Polymers80,0273
Non-polymers03
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9300 Å2
ΔGint-46 kcal/mol
Surface area25970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.764, 118.764, 118.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-8-

HOH

21A-51-

HOH

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Components

#1: Protein BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE / PROBABLE DIHYDROLIPOAMIDE S-ACETYLTRANSFERASE E2 COMPONENT PDHC (LIPOATE ACETYLTRANSFERASE) ...PROBABLE DIHYDROLIPOAMIDE S-ACETYLTRANSFERASE E2 COMPONENT PDHC (LIPOATE ACETYLTRANSFERASE) (THIOLTRANSACETYLASE A)


Mass: 26675.676 Da / Num. of mol.: 1 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 155-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pdhC, Rv2495c / Production host: Escherichia coli (E. coli)
References: UniProt: O06159, dihydrolipoyllysine-residue acetyltransferase
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% TASCIMATE, PH 7, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 18995 / % possible obs: 100 % / Observed criterion σ(I): -5 / Redundancy: 19.1 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.077 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 19.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.5.0089refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.247 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22217 979 5.2 %RANDOM
Rwork0.18185 ---
obs0.18387 17990 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.685 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1697 0 9 140 1846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221744
X-RAY DIFFRACTIONr_bond_other_d0.0010.021144
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9752380
X-RAY DIFFRACTIONr_angle_other_deg0.92132803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0885230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84223.18266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.915275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3151514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9211.51143
X-RAY DIFFRACTIONr_mcbond_other0.2081.5465
X-RAY DIFFRACTIONr_mcangle_it1.63321846
X-RAY DIFFRACTIONr_scbond_it2.1423601
X-RAY DIFFRACTIONr_scangle_it3.5454.5533
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 65 -
Rwork0.197 1323 -
obs--100 %

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