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- PDB-3e53: Crystal structure of N-terminal domain of a Fatty Acyl AMP Ligase... -

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Basic information

Entry
Database: PDB / ID: 3.0E+53
TitleCrystal structure of N-terminal domain of a Fatty Acyl AMP Ligase FAAL28 from Mycobacterium tuberculosis
ComponentsFATTY-ACID-CoA LIGASE FADD28
KeywordsLIGASE / Fatty acyl AMP Ligase / FadD28 / Mycobacterium tuberculosis
Function / homology
Function and homology information


long-chain fatty acid adenylyltransferase FadD28 / Dimycocersyl phthiocerol biosynthesis / adenylyltransferase activity / symbiont-mediated suppression of host innate immune response / DIM/DIP cell wall layer assembly / fatty-acyl-CoA synthase activity / response to host immune response / biological process involved in interaction with host / lipid biosynthetic process / ligase activity ...long-chain fatty acid adenylyltransferase FadD28 / Dimycocersyl phthiocerol biosynthesis / adenylyltransferase activity / symbiont-mediated suppression of host innate immune response / DIM/DIP cell wall layer assembly / fatty-acyl-CoA synthase activity / response to host immune response / biological process involved in interaction with host / lipid biosynthetic process / ligase activity / fatty acid biosynthetic process / ATP binding / plasma membrane / cytosol
Similarity search - Function
Fatty acyl-AMP ligase /fatty acyl-CoA ligase / ANL, N-terminal domain / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Long-chain-fatty-acid--AMP ligase FadD28 / Long-chain-fatty-acid--AMP ligase FadD28
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsGoyal, A. / Rajakumara, E. / Yousuf, M. / Sankaranarayanan, R.
CitationJournal: Nat.Chem.Biol. / Year: 2009
Title: Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis.
Authors: Arora, P. / Goyal, A. / Natarajan, V.T. / Rajakumara, E. / Verma, P. / Gupta, R. / Yousuf, M. / Trivedi, O.A. / Mohanty, D. / Tyagi, A. / Sankaranarayanan, R. / Gokhale, R.S.
History
DepositionAug 13, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FATTY-ACID-CoA LIGASE FADD28


Theoretical massNumber of molelcules
Total (without water)52,4601
Polymers52,4601
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.972, 60.740, 136.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FATTY-ACID-CoA LIGASE FADD28 / Fatty acyl AMP Ligase / FadD28 / FATTY-ACID-CoA SYNTHETASE / FATTY-ACID-CoA SYNTHASE / Acyl-CoA synthase


Mass: 52459.965 Da / Num. of mol.: 1 / Fragment: N-Terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: fadD28, MT3011, Rv2941 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P96290, UniProt: P9WQ59*PLUS, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG3350, Sodium MES, B-mercaptoethanol, Lithium sulphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9792, 0.9800, 0.9776
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 10, 2005 / Details: Mirrors (Rh coated, zerodur, vertical focussing)
RadiationMonochromator: Fixed exit double crystal Si[111], Horizontally focussing
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.981
30.97761
ReflectionResolution: 2.35→20 Å / Num. all: 18036 / Num. obs: 18036 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 21.87
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.36 / Num. unique all: 850 / % possible all: 95.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1480704.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 913 5.1 %RANDOM
Rwork0.207 ---
obs0.207 17986 99.4 %-
all-17986 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.103 Å2 / ksol: 0.350403 e/Å3
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.26 Å20 Å20 Å2
2---5.92 Å20 Å2
3----2.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3245 0 0 240 3485
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.722
X-RAY DIFFRACTIONc_scangle_it3.862.5
LS refinement shellResolution: 2.35→2.43 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.356 75 5 %
Rwork0.286 1436 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3mse_xplor_parammse_xplor_top

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