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- PDB-8hd4: Full-length crystal structure of mycobacterium tuberculosis FadD2... -

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Basic information

Entry
Database: PDB / ID: 8hd4
TitleFull-length crystal structure of mycobacterium tuberculosis FadD23 in complex with AMPC16
ComponentsLong-chain-fatty-acid--AMP ligase FadD23
KeywordsBIOSYNTHETIC PROTEIN / fatty-acid-AMP synthetase
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
palmitoyl adenylate / Long-chain-fatty-acid--AMP ligase FadD23
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsYan, M.R. / Liu, X. / Zhang, W. / Rao, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7882
Polymers65,2021
Non-polymers5861
Water59433
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)73.582, 73.582, 462.593
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 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-1TF / palmitoyl adenylate / 5'-O-[(R)-(hexadecanoyloxy)(hydroxy)phosphoryl]adenosine


Mass: 585.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H44N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 140 mM sodium citrate tribasic dihydrate, 60 mM magnesium chloride hexahydrate, 30 mM tris hydrochloride pH 8.5, 14% (w/v) polyethylene glycol 3350, and 9% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.68→45.87 Å / Num. obs: 22247 / % possible obs: 99.8 % / Redundancy: 9.895 % / Biso Wilson estimate: 68.607 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.11 / Χ2: 0.878 / Net I/σ(I): 13.7 / Num. measured all: 388631
Reflection shellResolution: 2.68→2.85 Å / Redundancy: 9.349 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.22 / Num. unique obs: 6305 / CC1/2: 0.915 / Rrim(I) all: 0.454 / % possible all: 99.2

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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: 2.68→45.87 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 1121 5.07 %
Rwork0.2137 --
obs0.2157 22117 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.68→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 40 33 4173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.810.41711450.37472507X-RAY DIFFRACTION99
2.81-2.950.34951300.29992551X-RAY DIFFRACTION100
2.95-3.140.34561550.26652533X-RAY DIFFRACTION100
3.14-3.380.32891290.27462582X-RAY DIFFRACTION100
3.38-3.720.261350.22892599X-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)
12.314-0.4571-0.16052.12590.28672.18140.04710.0429-0.2778-0.23280.0554-0.10660.260.1435-0.10060.3413-0.04360.00280.49-0.0010.422442.825220.6165219.9163
21.66950.2475-0.23012.6651-0.05241.2867-0.1725-0.21790.0299-0.14830.15030.1458-0.1951-0.21220.02220.3788-0.0157-0.04990.57740.03080.373133.007142.8019219.6049
32.7788-0.17920.16921.615-0.23863.0344-0.3793-0.0786-0.12170.4946-0.09590.22270.5164-0.18980.54980.6681-0.0480.10410.4503-0.03430.488937.872153.4273204.7824
42.13121.4046-0.94823.3580.47042.8727-0.46340.1332-0.6170.2063-0.17980.06740.988-0.13480.45130.7408-0.01290.1580.4897-0.04630.678737.99149.5615194.6753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 235 )
2X-RAY DIFFRACTION2chain 'A' and (resid 236 through 459 )
3X-RAY DIFFRACTION3chain 'A' and (resid 460 through 496 )
4X-RAY DIFFRACTION4chain 'A' and (resid 497 through 575 )

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