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- PDB-8hdf: Full length crystal structure of mycobacterium tuberculosis FadD2... -

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Basic information

Entry
Database: PDB / ID: 8hdf
TitleFull length crystal structure of mycobacterium tuberculosis FadD23 in complex with ANP and PLM
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PALMITIC ACID / Long-chain-fatty-acid--AMP ligase FadD23
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 4, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,9653
Polymers65,2021
Non-polymers7632
Water1,26170
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)72.837, 72.837, 457.908
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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: 65202.023 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: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 70 mM Tris pH 8.5, 140 mM sodium citrate tribasic dihydrate, 140 mM ammonium phosphate monobasic, 35% w/v (+/-)-2-methyl-2,4-pentanediol, and 14% (w/v) polyethylene glycol 3350

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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: Nov 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 36391 / % possible obs: 99.9 % / Redundancy: 7.13 % / CC1/2: 0.99 / Net I/σ(I): 21.13
Reflection shellResolution: 2.24→2.38 Å / Num. unique obs: 10499 / CC1/2: 0.865 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIXv1.20.1refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+53 / Resolution: 2.24→45.41 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 1803 4.98 %
Rwork0.2059 --
obs0.2083 36228 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 49 70 4234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084254
X-RAY DIFFRACTIONf_angle_d0.9775803
X-RAY DIFFRACTIONf_dihedral_angle_d12.036601
X-RAY DIFFRACTIONf_chiral_restr0.055671
X-RAY DIFFRACTIONf_plane_restr0.006748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.30.33511340.2892539X-RAY DIFFRACTION99
2.3-2.370.33871300.27272585X-RAY DIFFRACTION100
2.37-2.450.35261520.26472566X-RAY DIFFRACTION100
2.45-2.530.30551300.25482581X-RAY DIFFRACTION100
2.53-2.630.29971400.25562588X-RAY DIFFRACTION100
2.63-2.750.29151400.24862590X-RAY DIFFRACTION100
2.75-2.90.27821330.25132622X-RAY DIFFRACTION100
2.9-3.080.311390.25492618X-RAY DIFFRACTION100
3.08-3.320.26991460.23492659X-RAY DIFFRACTION100
3.32-3.650.2651420.21192647X-RAY DIFFRACTION100
3.65-4.180.22921290.18292687X-RAY DIFFRACTION100
4.18-5.270.23531340.16012770X-RAY DIFFRACTION100
5.27-45.410.22131540.19162973X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.67660.00540.19961.44180.19322.47750.00130.094-0.1982-0.20930.1185-0.12470.27210.0155-0.0010.3583-0.01550.02730.5496-0.10050.529844.703816.9839215.2789
20.48510.1015-0.17991.2711-0.07310.9417-0.13430.1185-0.084-0.21910.11050.1338-0.0602-0.15910.00020.2724-0.059-0.04460.6706-0.04170.435827.585832.2806216.055
30.6879-0.3747-0.28471.7426-0.16540.848-0.021-0.5490.1556-0.13110.0905-0.1718-0.24250.0540.00050.3267-0.0304-0.01590.565-0.14520.409340.743451.3242222.2754
40.46310.11930.28320.7262-0.42390.4863-0.2638-0.0406-0.15390.5969-0.4137-0.27460.1627-0.1249-0.12310.7232-0.04790.19640.5028-0.1480.519436.999153.2155202.6597
51.39560.2697-0.41311.92030.51111.7856-0.33130.0181-0.03560.6356-0.05260.25030.8289-0.0433-0.00660.73590.01550.16260.45-0.08950.507637.004449.3885192.768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 179 )
2X-RAY DIFFRACTION2chain 'A' and (resid 180 through 348 )
3X-RAY DIFFRACTION3chain 'A' and (resid 349 through 459 )
4X-RAY DIFFRACTION4chain 'A' and (resid 460 through 496 )
5X-RAY DIFFRACTION5chain 'A' and (resid 497 through 575 )

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