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- PDB-8hcz: N-terminal domain structure of mycobacterium tuberculosis FadD23 -

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Basic information

Entry
Database: PDB / ID: 8hcz
TitleN-terminal domain structure of mycobacterium tuberculosis FadD23
ComponentsLong-chain-fatty-acid--AMP ligase FadD23
KeywordsBIOSYNTHETIC PROTEIN / Long-chain-fatty-acid--AMP ligase
Function / homology
Function and homology information


long-chain fatty acid adenylase/transferase FadD23 / sulfolipid biosynthetic process / adenylyltransferase activity / Actinobacterium-type cell wall biogenesis / ligase activity / fatty acid biosynthetic process / ATP binding / membrane
Similarity search - Function
Fatty acyl-AMP ligase /fatty acyl-CoA ligase / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
Long-chain-fatty-acid--AMP ligase FadD23
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsYan, M.R. / Liu, X. / Zhang, W. / Rao, Z.H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)32100142 China
National Natural Science Foundation of China (NSFC)32171259 China
CitationJournal: Front Microbiol / Year: 2023
Title: The Key Roles of Mycobacterium tuberculosis FadD23 C-terminal Domain in Catalytic Mechanisms.
Authors: Yan, M. / Cao, L. / Zhao, L. / Zhou, W. / Liu, X. / Zhang, W. / Rao, Z.
History
DepositionNov 3, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Long-chain-fatty-acid--AMP ligase FadD23


Theoretical massNumber of molelcules
Total (without water)52,2911
Polymers52,2911
Non-polymers00
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.924, 72.595, 90.800
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 FadD23 / FAAL23 / Long-chain fatty acid adenylyltransferase FadD23 / Long-chain-fatty-acid adenylase/transferase FadD23


Mass: 52291.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: fadD23, Rv3826 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WQ47, long-chain fatty acid adenylase/transferase FadD23
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 70mM Bis-Tris pH6.5, 60mM Sodium chloride, 20% (w/v) polyethylene glycol 3,350, 6%(w/v) polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.48→45.4 Å / Num. obs: 73763 / % possible obs: 97.8 % / Redundancy: 6.9 % / CC1/2: 0.98 / Net I/σ(I): 7.97
Reflection shellResolution: 1.48→1.57 Å / Num. unique obs: 72121 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+53 / Resolution: 1.48→45.4 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1686 3650 5.06 %
Rwork0.1452 --
obs0.1464 72121 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.48→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 0 390 3754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123446
X-RAY DIFFRACTIONf_angle_d1.1274706
X-RAY DIFFRACTIONf_dihedral_angle_d5.385478
X-RAY DIFFRACTIONf_chiral_restr0.095538
X-RAY DIFFRACTIONf_plane_restr0.009615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.24631320.19212439X-RAY DIFFRACTION92
1.5-1.520.18991240.15572600X-RAY DIFFRACTION97
1.52-1.550.18841290.14852543X-RAY DIFFRACTION96
1.55-1.570.20461160.14242620X-RAY DIFFRACTION97
1.57-1.590.22241290.13752594X-RAY DIFFRACTION97
1.59-1.620.19211550.13012532X-RAY DIFFRACTION96
1.62-1.650.16191580.11952556X-RAY DIFFRACTION97
1.65-1.680.16331460.11972582X-RAY DIFFRACTION97
1.68-1.710.15441450.11872588X-RAY DIFFRACTION97
1.71-1.740.16921180.12132614X-RAY DIFFRACTION97
1.74-1.780.1661480.11812598X-RAY DIFFRACTION98
1.78-1.820.15041660.11552590X-RAY DIFFRACTION98
1.82-1.870.1651360.12142615X-RAY DIFFRACTION98
1.87-1.920.14881280.12152632X-RAY DIFFRACTION98
1.92-1.980.16321370.12642646X-RAY DIFFRACTION98
1.98-2.040.17181470.13532616X-RAY DIFFRACTION98
2.04-2.110.17151430.13722648X-RAY DIFFRACTION98
2.11-2.20.18261470.13832631X-RAY DIFFRACTION98
2.2-2.30.14951620.14092647X-RAY DIFFRACTION99
2.3-2.420.16871280.14752690X-RAY DIFFRACTION99
2.42-2.570.1781380.16142673X-RAY DIFFRACTION99
2.57-2.770.17021300.16212707X-RAY DIFFRACTION99
2.77-3.050.18331610.16142703X-RAY DIFFRACTION99
3.05-3.490.171440.16122723X-RAY DIFFRACTION100
3.49-4.390.1431380.14222774X-RAY DIFFRACTION100
4.39-45.40.17271450.16222910X-RAY DIFFRACTION100

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