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- PDB-1scz: Improved structural model for the catalytic domain of E.coli dihy... -

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Basic information

Entry
Database: PDB / ID: 1scz
TitleImproved structural model for the catalytic domain of E.coli dihydrolipoamide succinyltransferase
ComponentsDihydrolipoamide Succinyltransferase
KeywordsTRANSFERASE / CoA-dependent acyltransferase / CAT-like / alpha and beta (2 layers) / mixed beta-sheeet of 6 strands
Function / homology
Function and homology information


L-lysine catabolic process to acetyl-CoA via saccharopine / oxoglutarate dehydrogenase complex / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / lipoic acid binding / tricarboxylic acid cycle / cytosol / cytoplasm
Similarity search - Function
Dihydrolipoamide succinyltransferase / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain ...Dihydrolipoamide succinyltransferase / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 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
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex / Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsSchormann, N. / Symersky, J. / Carson, M. / Luo, M. / Tsao, J. / Johnson, D. / Huang, W.-Y. / Pruett, P. / Lin, G. / Li, S. ...Schormann, N. / Symersky, J. / Carson, M. / Luo, M. / Tsao, J. / Johnson, D. / Huang, W.-Y. / Pruett, P. / Lin, G. / Li, S. / Qiu, S. / Arabashi, A. / Bunzel, B. / Luo, D. / Nagy, L. / Gray, R. / Luan, C.-H. / Zhang, Z. / Lu, S. / DeLucas, L.
CitationJournal: To be Published
Title: Improved structural model for the catalytic domain of E.coli dihydrolipoamide succinyltransferase
Authors: Schormann, N. / Symersky, J. / Carson, M. / Luo, M. / Tsao, J. / Johnson, D. / Huang, W.-Y. / Pruett, P. / Lin, G. / Li, S. / Qiu, S. / Arabashi, A. / Bunzel, B. / Luo, D. / Nagy, L. / Gray, ...Authors: Schormann, N. / Symersky, J. / Carson, M. / Luo, M. / Tsao, J. / Johnson, D. / Huang, W.-Y. / Pruett, P. / Lin, G. / Li, S. / Qiu, S. / Arabashi, A. / Bunzel, B. / Luo, D. / Nagy, L. / Gray, R. / Luan, C.-H. / Zhang, Z. / Lu, S. / DeLucas, L.
History
DepositionFeb 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrolipoamide Succinyltransferase


Theoretical massNumber of molelcules
Total (without water)26,1071
Polymers26,1071
Non-polymers00
Water3,945219
1
A: Dihydrolipoamide Succinyltransferase
x 24


Theoretical massNumber of molelcules
Total (without water)626,57824
Polymers626,57824
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_566-x,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation57_455y-1/2,z,x+1/21
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation59_465y-1/2,-z+1,-x+1/21
crystal symmetry operation60_565-y+1/2,-z+1,x+1/21
crystal symmetry operation69_455z-1/2,y,-x+1/21
crystal symmetry operation70_465z-1/2,-y+1,x+1/21
crystal symmetry operation71_555-z+1/2,y,x+1/21
crystal symmetry operation72_565-z+1/2,-y+1,-x+1/21
crystal symmetry operation77_455z-1/2,x+1/2,y1
crystal symmetry operation78_456z-1/2,-x+1/2,-y+11
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
crystal symmetry operation80_556-z+1/2,x+1/2,-y+11
crystal symmetry operation85_456y-1/2,x+1/2,-z+11
crystal symmetry operation86_556-y+1/2,-x+1/2,-z+11
crystal symmetry operation87_455y-1/2,-x+1/2,z1
crystal symmetry operation88_555-y+1/2,x+1/2,z1
Buried area93740 Å2
ΔGint-552 kcal/mol
Surface area240590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.576, 220.576, 220.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Cell settingcubic
Space group name H-MF432

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Components

#1: Protein Dihydrolipoamide Succinyltransferase / E.C.2.3.1.61 / E2


Mass: 26107.420 Da / Num. of mol.: 1 / Fragment: catalytic domain, residues 172-404
Source method: isolated from a genetically manipulated source
Details: component of 2-oxoglutarate dehydrogenase complex / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: SUCB / Plasmid: pET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P07016, UniProt: P0AFG6*PLUS, dihydrolipoyllysine-residue succinyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 3.9 Å3/Da / Density % sol: 68.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% PEG 4000,0.05M Hepes, 0.2M Ammonium acetate, 0.15M Magnesium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99997 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 25, 2003 / Details: Mirrors
RadiationMonochromator: Double Crystal Monochromator SI-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 23922 / Num. obs: 23922 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 43.1 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 7.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 43 % / Rmerge(I) obs: 0.3 / Num. unique all: 2315 / Rsym value: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
SHELXSphasing
CNS1.1refinement
RefinementMethod to determine structure: SIRAS
Starting model: starting model was a model built by Resolve and Arp_Warp using phases obtained from an iodide derivative

Resolution: 2.2→19.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 212682.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1120 4.9 %RANDOM
Rwork0.211 ---
all0.2141 22962 --
obs0.214 22962 96.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.5984 Å2 / ksol: 0.34062 e/Å3
Displacement parametersBiso mean: 28.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 0 219 2046
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it2.532
X-RAY DIFFRACTIONc_scangle_it3.82.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 163 4.5 %
Rwork0.206 3432 -
obs-3432 92.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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