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- PDB-3t5a: Crystal structure of N-terminal domain of FAAL28 G330W mutant fro... -

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Basic information

Entry
Database: PDB / ID: 3t5a
TitleCrystal structure of N-terminal domain of FAAL28 G330W mutant from Mycobacterium tuberculosis
ComponentsLong-chain-fatty-acid--AMP ligase FadD28
KeywordsLIGASE / Acetyl-CoA synthetase like fold / AMP-binding
Function / homology
Function and homology information


long-chain fatty acid adenylyltransferase FadD28 / Dimycocersyl phthiocerol biosynthesis / adenylyltransferase activity / fatty-acyl-CoA synthase activity / response to host immune response / DIM/DIP cell wall layer assembly / biological process involved in interaction with host / lipid biosynthetic process / ligase activity / fatty acid biosynthetic process ...long-chain fatty acid adenylyltransferase FadD28 / Dimycocersyl phthiocerol biosynthesis / adenylyltransferase activity / fatty-acyl-CoA synthase activity / response to host immune response / DIM/DIP cell wall layer assembly / biological process involved in interaction with host / lipid biosynthetic process / ligase activity / fatty acid biosynthetic process / symbiont-mediated suppression of host innate immune response / ATP binding / plasma membrane / cytosol
Similarity search - Function
: / Disco-interacting protein 2-like, AMP domain / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold ...: / Disco-interacting protein 2-like, AMP domain / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / 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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGoyal, A. / Sankaranarayanan, R.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Molecular basis of the functional divergence of fatty acyl-AMP ligase biosynthetic enzymes of Mycobacterium tuberculosis.
Authors: Goyal, A. / Verma, P. / Anandhakrishnan, M. / Gokhale, R.S. / Sankaranarayanan, R.
History
DepositionJul 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Long-chain-fatty-acid--AMP ligase FadD28


Theoretical massNumber of molelcules
Total (without water)52,0731
Polymers52,0731
Non-polymers00
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.207, 60.317, 137.773
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 Long-chain-fatty-acid--AMP ligase FadD28 / FAAL / Acyl-AMP synthetase


Mass: 52073.285 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP RESIDUES 1-460) / Mutation: G330W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: acoas, 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


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 18% PEG 3350, 0.1M Sodium MES, 5% ethylene glycol, 0.15M Lithium sulphate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 28, 2008 / Details: Osmic mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 25902 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 31.69 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.63
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.03 / Num. unique all: 2564 / % possible all: 94

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3E53

3e53


Resolution: 2.05→25 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.27 1291 RANDOM
Rwork0.216 --
obs0.216 25606 -
all-25606 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.382 Å20 Å20 Å2
2--7.044 Å20 Å2
3----1.662 Å2
Refinement stepCycle: LAST / Resolution: 2.05→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 323 3689

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