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- PDB-7wua: Crystal structures of FadD32 from Corynebacterium diphtheriae -

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Basic information

Entry
Database: PDB / ID: 7wua
TitleCrystal structures of FadD32 from Corynebacterium diphtheriae
ComponentsAcyl-CoA synthase
KeywordsLIGASE / Fatty acid coa ligase
Function / homologyANL, C-terminal domain / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / MYRISTIC ACID / :
Function and homology information
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.999 Å
AuthorsLiu, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem Biophys Res Commun / Year: 2022
Title: Crystal structures of FadD32 and pks13-ACP domain from Corynebacterium diphtheriae
Authors: Chen, R. / Yuan, J. / Shi, X. / Tang, W.
History
DepositionFeb 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,69514
Polymers262,7084
Non-polymers2,98710
Water34,8231933
1
A: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4364
Polymers65,6771
Non-polymers7593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-1 kcal/mol
Surface area24940 Å2
MethodPISA
2
B: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4364
Polymers65,6771
Non-polymers7593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-1 kcal/mol
Surface area24870 Å2
MethodPISA
3
C: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4123
Polymers65,6771
Non-polymers7352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint0 kcal/mol
Surface area25730 Å2
MethodPISA
4
D: Acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4123
Polymers65,6771
Non-polymers7352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-0 kcal/mol
Surface area21080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.647, 97.535, 142.043
Angle α, β, γ (deg.)90.000, 95.930, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acyl-CoA synthase


Mass: 65676.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: CIP107532_02306 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A679LZK7
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1933 / 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: 2.85 Å3/Da / Density % sol: 56.83 % / Mosaicity: 0.287 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8
Details: 0.1 M NaCl, 0.1 M Bis-Tris pH 6.5, 1.5 M (NH4)2SO4 , VAPOR DIFFUSION, Sitting DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9783 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. obs: 198544 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.056 / Rrim(I) all: 0.124 / Χ2: 0.93 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.034.70.64498270.7350.330.7250.76399.7
2.03-2.074.60.53798890.7530.2780.6070.83599.8
2.07-2.114.40.46598700.8090.2480.5290.8499.8
2.11-2.154.70.42899050.8610.2180.4820.85199.8
2.15-2.24.70.36398400.8870.1860.4090.87399.8
2.2-2.254.50.31999190.8960.1670.3620.99499.7
2.25-2.314.90.29299030.9260.1450.3270.93199.9
2.31-2.374.90.24898280.9410.1240.2780.94699.3
2.37-2.444.90.22398840.9480.1120.250.94299.9
2.44-2.524.80.19299180.9570.0970.2160.945100
2.52-2.614.70.17399410.9640.0880.1950.955100
2.61-2.714.50.15299490.9670.080.1730.964100
2.71-2.844.80.13698960.9750.0690.1520.946100
2.84-2.994.60.12498980.9760.0640.140.934100
2.99-3.1750.11699650.9790.0580.130.987100
3.17-3.424.90.10599550.9810.0530.1180.986100
3.42-3.764.70.1100050.9830.0520.1131.06599.9
3.76-4.314.60.09499750.9840.0490.1061.0399.9
4.31-5.434.80.089100370.9860.0450.10.95599.9
5.43-504.60.081101400.9910.0420.0920.84799.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hm3

5hm3


Resolution: 1.999→46.099 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 9562 4.94 %
Rwork0.1849 184045 -
obs0.1868 193607 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.2 Å2 / Biso mean: 28.1692 Å2 / Biso min: 6.33 Å2
Refinement stepCycle: final / Resolution: 1.999→46.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17485 0 350 1933 19768
Biso mean--31.54 34.17 -
Num. residues----2283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.999-2.02160.28632020.251412666
2.0216-2.04540.29792750.2357517682
2.0454-2.07040.28962940.2309559489
2.0704-2.09660.29152990.2225576092
2.0966-2.12420.26613070.2166610996
2.1242-2.15330.25673200.2059622099
2.1533-2.1840.23913430.2012618499
2.184-2.21660.26343410.1942620999
2.2166-2.25130.2453440.1969616499
2.2513-2.28820.2463230.26267100
2.2882-2.32760.25073290.19196299100
2.3276-2.36990.25433150.1826620699
2.3699-2.41550.22853250.18666298100
2.4155-2.46480.23163140.18626285100
2.4648-2.51840.24962930.18216328100
2.5184-2.5770.24343090.1856322100
2.577-2.64140.21493440.18886251100
2.6414-2.71280.24063130.18826324100
2.7128-2.79270.24723250.18846267100
2.7927-2.88280.22793390.19456268100
2.8828-2.98580.24523390.19756302100
2.9858-3.10530.26173620.19636329100
3.1053-3.24660.2093460.18566294100
3.2466-3.41770.20723090.17896305100
3.4177-3.63180.22863490.17566329100
3.6318-3.91210.19333300.16146321100
3.9121-4.30550.15943190.15476337100
4.3055-4.92790.16883150.15016371100
4.9279-6.20620.20463190.18396382100
6.2062-46.0990.22763200.2021641898

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