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- PDB-5ey8: Structure of FadD32 from Mycobacterium smegmatis complexed to AMPC20 -

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Basic information

Entry
Database: PDB / ID: 5ey8
TitleStructure of FadD32 from Mycobacterium smegmatis complexed to AMPC20
ComponentsAcyl-CoA synthase
KeywordsLIGASE / fatty-acyl AMP ligase
Function / homology
Function and homology information


long-chain-fatty-acid-[acyl-carrier-protein] ligase / long-chain fatty acid [acyl-carrier-protein] ligase activity / lipid biosynthetic process / fatty acid metabolic process / ATP binding
Similarity search - Function
: / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold ...: / Fatty acyl-AMP ligase /fatty acyl-CoA ligase / ANL, C-terminal domain / ANL, N-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5SV / Long-chain-fatty-acid--AMP ligase FadD32
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsGuillet, V. / Maveyraud, L. / Mourey, L.
Funding support1items
OrganizationGrant numberCountry
European CommunityNew Medicines for Tuberculosis (grant LSHP-CT-2005-018923
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Insight into Structure-Function Relationships and Inhibition of the Fatty Acyl-AMP Ligase (FadD32) Orthologs from Mycobacteria.
Authors: Guillet, V. / Galandrin, S. / Maveyraud, L. / Ladeveze, S. / Mariaule, V. / Bon, C. / Eynard, N. / Daffe, M. / Marrakchi, H. / Mourey, L.
History
DepositionNov 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA synthase
B: Acyl-CoA synthase
C: Acyl-CoA synthase
D: Acyl-CoA synthase
E: Acyl-CoA synthase
F: Acyl-CoA synthase
G: Acyl-CoA synthase
H: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)551,65818
Polymers546,4528
Non-polymers5,20610
Water00
1
A: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9342
Polymers68,3071
Non-polymers6281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9342
Polymers68,3071
Non-polymers6281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9342
Polymers68,3071
Non-polymers6281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9342
Polymers68,3071
Non-polymers6281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0263
Polymers68,3071
Non-polymers7202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0263
Polymers68,3071
Non-polymers7202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9342
Polymers68,3071
Non-polymers6281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9342
Polymers68,3071
Non-polymers6281
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.040, 164.040, 231.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
Acyl-CoA synthase / Fatty-acid-CoA ligase FadD32


Mass: 68306.500 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: fadD32, MSMEG_6393, MSMEI_6225 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star One Shot / References: UniProt: A0R618
#2: Chemical
ChemComp-5SV / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate


Mass: 627.753 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C30H54N5O7P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / Details: PEG 1000 TrisHCl 100 mM, pH 8.2 - 8.7 / PH range: 8.2-8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.5→51.2 Å / Num. all: 72026 / Num. obs: 72026 / % possible obs: 93.9 % / Redundancy: 3 % / Rsym value: 0.232 / Net I/σ(I): 4.6
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.6 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction
RefinementResolution: 3.5→49.442 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 3632 5.04 %random selection
Rwork0.2227 ---
obs0.2259 72002 93.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→49.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33081 0 297 0 33378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534200
X-RAY DIFFRACTIONf_angle_d1.01147046
X-RAY DIFFRACTIONf_dihedral_angle_d12.35511140
X-RAY DIFFRACTIONf_chiral_restr0.0385423
X-RAY DIFFRACTIONf_plane_restr0.0056414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.54610.37291410.3092663X-RAY DIFFRACTION96
3.5461-3.59460.33431520.29262678X-RAY DIFFRACTION95
3.5946-3.6460.35281280.29132698X-RAY DIFFRACTION95
3.646-3.70040.38611480.27822625X-RAY DIFFRACTION96
3.7004-3.75820.32891370.27822682X-RAY DIFFRACTION95
3.7582-3.81980.36021270.26642661X-RAY DIFFRACTION95
3.8198-3.88560.35241610.25462650X-RAY DIFFRACTION96
3.8856-3.95620.32531440.26072616X-RAY DIFFRACTION95
3.9562-4.03230.30751490.24042640X-RAY DIFFRACTION94
4.0323-4.11460.30021320.23892704X-RAY DIFFRACTION94
4.1146-4.2040.32221310.22992651X-RAY DIFFRACTION94
4.204-4.30170.2711220.21342671X-RAY DIFFRACTION95
4.3017-4.40920.25131440.20042643X-RAY DIFFRACTION94
4.4092-4.52840.27551390.18962611X-RAY DIFFRACTION94
4.5284-4.66150.24921360.18722677X-RAY DIFFRACTION94
4.6615-4.81190.23571490.18832620X-RAY DIFFRACTION94
4.8119-4.98370.25631270.19952623X-RAY DIFFRACTION93
4.9837-5.1830.25531570.20612600X-RAY DIFFRACTION94
5.183-5.41860.28131380.20712620X-RAY DIFFRACTION93
5.4186-5.70390.29441540.21962579X-RAY DIFFRACTION93
5.7039-6.06070.31121320.21772613X-RAY DIFFRACTION92
6.0607-6.52770.29681410.22622570X-RAY DIFFRACTION92
6.5277-7.18280.26671540.2122597X-RAY DIFFRACTION91
7.1828-8.21810.24751300.19182583X-RAY DIFFRACTION91
8.2181-10.33830.22651310.17242568X-RAY DIFFRACTION91
10.3383-49.4470.25341280.22542527X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 35.077 Å / Origin y: 43.4777 Å / Origin z: 212.2505 Å
111213212223313233
T0.4502 Å20.0052 Å2-0.0129 Å2-0.4567 Å20.0083 Å2--0.4756 Å2
L-0.0142 °20.0098 °20.0078 °2--0.0057 °20.0099 °2--0.1644 °2
S-0.0067 Å °0.0123 Å °-0.001 Å °-0.0184 Å °0.0088 Å °0.0009 Å °-0.0388 Å °-0.0027 Å °-0.0104 Å °
Refinement TLS groupSelection details: all

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