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- PDB-5zrn: Inhibitor bound crystal structure of N-terminal domain of FACL13 ... -

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Basic information

Entry
Database: PDB / ID: 5zrn
TitleInhibitor bound crystal structure of N-terminal domain of FACL13 from Mycobacterium tuberculosis
ComponentsLong-chain-fatty-acid--CoA ligase FadD13
KeywordsLIGASE / Fatty acyl CoA Ligase / Inhibitor / FACL13 / Mycobacterium tuberculosis / lipid metabolism
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
5'-O-{[(1R)-1-hydroxydodecyl]sulfamoyl}adenosine / Long-chain-fatty-acid--CoA ligase FadD13
Similarity search - Component
Biological speciesMycobacterium tuberculosis CDC1551 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsGoyal, A. / Sankaranarayanan, R.
Funding support India, 1items
OrganizationGrant numberCountry
India
CitationJournal: To Be Published
Title: Inhibitor bound crystal structure of N-terminal domain of FACL13 from Mycobacterium tuberculosis
Authors: Goyal, A. / Sankaranarayanan, R.
History
DepositionApr 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Long-chain-fatty-acid--CoA ligase FadD13
B: Long-chain-fatty-acid--CoA ligase FadD13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2864
Polymers86,2242
Non-polymers1,0612
Water10,124562
1
A: Long-chain-fatty-acid--CoA ligase FadD13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6432
Polymers43,1121
Non-polymers5311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Long-chain-fatty-acid--CoA ligase FadD13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6432
Polymers43,1121
Non-polymers5311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.647, 129.647, 185.965
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Long-chain-fatty-acid--CoA ligase FadD13 / Fatty acyl-CoA ligase / FACL13 / Fatty acyl-CoA synthetase / FACS / Very-long-chain fatty-acyl-CoA ...Fatty acyl-CoA ligase / FACL13 / Fatty acyl-CoA synthetase / FACS / Very-long-chain fatty-acyl-CoA synthetase / ACSVL


Mass: 43112.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria)
Strain: CDC 1551 / Oshkosh / Gene: fadD13, MT3174 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WQ36, long-chain-fatty-acid-CoA ligase
#2: Chemical ChemComp-JSA / 5'-O-{[(1R)-1-hydroxydodecyl]sulfamoyl}adenosine


Mass: 530.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H38N6O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 25% Polyethylene glycol 3350, 0.1M Na-HEPES (pH 7.5), 0.1M Phenol

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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: Sep 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.37→25 Å / Num. obs: 32482 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.143 / Χ2: 0.65 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.37-2.456.90.67231880.608199.9
2.45-2.557.30.580.6211100
2.55-2.677.40.5210.6181100
2.67-2.817.50.3790.641100
2.81-2.997.50.2930.6281100
2.99-3.227.50.2010.6151100
3.22-3.547.50.1380.651100
3.54-4.057.50.080.6931100
4.05-5.097.50.0560.7041100
5.09-257.20.0470.7181100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T5B

3t5b


Resolution: 2.37→25 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 1612 5 %Random selection
Rwork0.1976 ---
obs-32436 100 %-
Solvent computationBsol: 41.6171 Å2
Displacement parametersBiso max: 70.85 Å2 / Biso mean: 30.448 Å2 / Biso min: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1-2.597 Å20 Å20 Å2
2--2.597 Å20 Å2
3----5.194 Å2
Refinement stepCycle: final / Resolution: 2.37→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6052 0 72 562 6686
Biso mean--46.71 36.75 -
Num. residues----796
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3451.5
X-RAY DIFFRACTIONc_scbond_it2.0552
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scangle_it2.9992.5
LS refinement shellResolution: 2.37→2.4 Å / Rfactor Rfree: 0.3217 / Rfactor Rwork: 0.2762
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2lsa.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

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