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- PDB-5d6n: Crystal structure of a mycobacterial protein -

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Basic information

Entry
Database: PDB / ID: 5d6n
TitleCrystal structure of a mycobacterial protein
ComponentsAcyl-CoA synthase
KeywordsLIGASE / Mycobacterium smegmatis
Function / homology
Function and homology information


long-chain-fatty-acid-[acyl-carrier-protein] ligase / long-chain fatty acid [acyl-carrier-protein] ligase activity / adenylyltransferase activity / fatty acid biosynthetic process / ATP binding / plasma membrane
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 / 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 FadD32
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsLi, W.J. / Bi, L.J.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: Sci Rep / Year: 2015
Title: Crystal structure of FadD32, an enzyme essential for mycolic acid biosynthesis in mycobacteria.
Authors: Li, W. / Gu, S. / Fleming, J. / Bi, L.
History
DepositionAug 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-CoA synthase


Theoretical massNumber of molelcules
Total (without water)55,4431
Polymers55,4431
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.680, 78.174, 102.157
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 Acyl-CoA synthase / Fatty-acid-CoA ligase FadD32


Mass: 55442.922 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: fadD32, MSMEG_6393, MSMEI_6225 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R618
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 289 K / Method: evaporation / Details: 0.1 M magnesium formate, 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19911 / % possible obs: 99.8 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 17.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.554 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+53 / Resolution: 2.401→25.675 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 1985 10 %
Rwork0.1845 --
obs0.1903 19858 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.401→25.675 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3691 0 0 290 3981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023789
X-RAY DIFFRACTIONf_angle_d0.6295173
X-RAY DIFFRACTIONf_dihedral_angle_d12.1761360
X-RAY DIFFRACTIONf_chiral_restr0.024569
X-RAY DIFFRACTIONf_plane_restr0.003688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.401-2.4610.30571390.21371249X-RAY DIFFRACTION99
2.461-2.52750.34651370.23891238X-RAY DIFFRACTION100
2.5275-2.60180.31411410.23551259X-RAY DIFFRACTION100
2.6018-2.68570.30091390.22361263X-RAY DIFFRACTION100
2.6857-2.78150.30581410.23091255X-RAY DIFFRACTION100
2.7815-2.89280.28691380.22911252X-RAY DIFFRACTION100
2.8928-3.02420.26621430.2181277X-RAY DIFFRACTION100
3.0242-3.18340.27821390.22021261X-RAY DIFFRACTION100
3.1834-3.38240.23961410.18641267X-RAY DIFFRACTION100
3.3824-3.64290.21711430.17191292X-RAY DIFFRACTION100
3.6429-4.00830.23991410.15171268X-RAY DIFFRACTION100
4.0083-4.58540.19631450.14921300X-RAY DIFFRACTION100
4.5854-5.76630.2181440.15561313X-RAY DIFFRACTION100
5.7663-25.67680.17531540.16141379X-RAY DIFFRACTION100

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