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- PDB-3t5b: Crystal structure of N-terminal domain of FACL13 from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 3t5b
TitleCrystal structure of N-terminal domain of FACL13 from Mycobacterium tuberculosis
ComponentsPROBABLE CHAIN-FATTY-ACID-CoA LIGASE FADD13
KeywordsLIGASE / Acetyl-CoA synthetase like fold / AMP-binding
Function / homology
Function and homology information


long-chain-fatty-acid-CoA ligase / long-chain fatty acid-CoA ligase activity / medium-chain fatty acid-CoA ligase activity / fatty acid biosynthetic process / ATP binding / plasma membrane
Similarity search - Function
ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold ...ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / 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--CoA ligase FadD13 / Long-chain-fatty-acid--CoA ligase FadD13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 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
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: PROBABLE CHAIN-FATTY-ACID-CoA LIGASE FADD13


Theoretical massNumber of molelcules
Total (without water)42,8421
Polymers42,8421
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.878, 92.842, 96.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein PROBABLE CHAIN-FATTY-ACID-CoA LIGASE FADD13 / Substrate--CoA ligase / FATTY-ACYL-CoA SYNTHETASE


Mass: 42841.777 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP RESIDUES 1-396)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: fadD13, MT3174, Rv3089 / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O53306, UniProt: P9WQ36*PLUS, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Na-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: Dec 12, 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: 2.35→25 Å / Num. obs: 16344 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 28.17 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 9.13
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 2.09 / Num. unique all: 1606 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+53 / Resolution: 2.35→25 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.276 824 RANDOM
Rwork0.21 --
obs0.21 16243 -
all-16243 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.19 Å20 Å20 Å2
2---4.124 Å20 Å2
3----0.066 Å2
Refinement stepCycle: LAST / Resolution: 2.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 0 287 3294

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