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- PDB-7qf6: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transa... -

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Basic information

Entry
Database: PDB / ID: 7qf6
TitleN(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
ComponentsN(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
KeywordsTRANSFERASE / Hydroxyornithine transacylase
Function / homology
Function and homology information


N',N'',N'''-triacetylfusarinine C biosynthetic process / N-acyltransferase activity / siderophore biosynthetic process / ergosterol biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peroxisome
Similarity search - Function
Acyltransferase MbtK/IucB-like, conserved domain / Siderophore biosynthesis protein domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
: / THIOCYANATE ION / N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsPoonsiri, T. / Demitri, N. / Stefano, B.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development FundIPN95European Union
CitationJournal: To Be Published
Title: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
Authors: Poonsiri, T. / Demitri, N. / Stefano, B.
History
DepositionDec 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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

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Assembly

Deposited unit
A: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
B: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
C: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
D: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
E: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
F: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
G: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
H: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,89831
Polymers427,0228
Non-polymers1,87623
Water35,5441973
1
A: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
D: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
E: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
F: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,52916
Polymers213,5114
Non-polymers1,01812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24680 Å2
ΔGint-66 kcal/mol
Surface area63970 Å2
MethodPISA
2
B: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
C: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
G: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
H: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,36915
Polymers213,5114
Non-polymers85811
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24220 Å2
ΔGint-70 kcal/mol
Surface area64210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.274, 80.839, 179.840
Angle α, β, γ (deg.)101.170, 91.670, 117.250
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF / Hydroxyornithine transacylase sidF / Siderophore biosynthesis protein F


Mass: 53377.723 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: sidF, AFUA_3G03400 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4WF55, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1973 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18-20% PEG 3350, 0.2-0.24 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2021
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→174.82 Å / Num. obs: 313786 / % possible obs: 97.1 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Net I/σ(I): 17 / Num. measured all: 2129682 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.87-1.96.80.501104836153890.9290.2060.5433.696.2
10.24-174.825.90.0321124619040.9990.0140.03543.297.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
autoPROC1.0.5data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.87→174.82 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.189 / SU ML: 0.093 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 15716 5 %RANDOM
Rwork0.1719 ---
obs0.1737 298028 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.06 Å2 / Biso mean: 33.442 Å2 / Biso min: 14.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å21.85 Å2-0.56 Å2
2---0.12 Å2-1.17 Å2
3----2.58 Å2
Refinement stepCycle: final / Resolution: 1.87→174.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28760 0 116 1973 30849
Biso mean--43.37 34.79 -
Num. residues----3503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01229932
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.63840813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44953518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71320.7451812
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.136154536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.04915261
X-RAY DIFFRACTIONr_chiral_restr0.1420.23588
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0224060
LS refinement shellResolution: 1.87→1.919 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 1208 -
Rwork0.235 21838 -
all-23046 -
obs--96.27 %

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