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- PDB-3mae: CRYSTAL STRUCTURE OF PROBABLE DIHYDROLIPOAMIDE ACETYLTRANSFERASE ... -

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Basic information

Entry
Database: PDB / ID: 3mae
TitleCRYSTAL STRUCTURE OF PROBABLE DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM LISTERIA MONOCYTOGENES 4b F2365
Components2-oxoisovalerate dehydrogenase E2 component, dihydrolipoamide acetyltransferase
KeywordsTRANSFERASE / 2-oxoacid dehydrogenases acyltransferase / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / Acyltransferase / Lipoyl / New York SGX Research Center for Structural Genomics
Function / homologyChloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / 2-Layer Sandwich / Alpha Beta / PHOSPHATE ION / :
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsPatskovsky, Y. / Toro, R. / Gilmore, M. / 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 A CATALYTIC DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM LISTERIA MONOCYTOGENES 4b F2365
Authors: Patskovsky, Y. / Toro, R. / Gilmore, M. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
A: 2-oxoisovalerate dehydrogenase E2 component, dihydrolipoamide acetyltransferase
B: 2-oxoisovalerate dehydrogenase E2 component, dihydrolipoamide acetyltransferase
C: 2-oxoisovalerate dehydrogenase E2 component, dihydrolipoamide acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,18931
Polymers84,0883
Non-polymers2,10128
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15840 Å2
ΔGint-238 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.221, 173.008, 131.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

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Components

#1: Protein 2-oxoisovalerate dehydrogenase E2 component, dihydrolipoamide acetyltransferase


Mass: 28029.420 Da / Num. of mol.: 3 / Fragment: C-TERMINAL FRAGMENT, RESIDUES 172-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: F2365 / Gene: LMOf2365_1391 / Production host: Escherichia coli (E. coli)
References: UniProt: Q71ZU8, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.74 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100MM SODIUM CITRATE, PH 5.6, 1000MM AMMONIUM DIHYDROGEN PHOSPHATE, 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: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 3, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 43534 / % possible obs: 99.9 % / Observed criterion σ(I): -5 / Redundancy: 3.8 % / Biso Wilson estimate: 48.747 Å2 / Rsym value: 0.148 / Net I/σ(I): 4.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 0.8 / Rsym value: 0.96 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.124 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23362 1340 3.1 %RANDOM
Rwork0.19192 ---
obs0.19321 41830 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.671 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20 Å2
2---1.38 Å20 Å2
3---2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 0 112 68 5666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225661
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.9737635
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4945722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39725.022225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.106151038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6881526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214072
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.23123554
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.01435721
X-RAY DIFFRACTIONr_scbond_it5.83842107
X-RAY DIFFRACTIONr_scangle_it9.10861908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1714 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.420.5
Bmedium positional0.430.5
Cmedium positional0.370.5
Amedium thermal7.095
Bmedium thermal7.585
Cmedium thermal3.285
LS refinement shellResolution: 2.502→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 75 -
Rwork0.305 2872 -
obs--94.12 %

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