PDB-8kd8: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transa...

ID or keywords:

Entry

Database: PDB / ID: 8kd8

Title

N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF N-terminal domain

Components

N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF

Keywords

TRANSFERASE / GNAT / SidF / Aspergillus fumigatus / siderophore / acetyltransferase

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

Biological species

Aspergillus fumigatus (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.581 Å

Authors

Poonsiri, T. / Demitri, N. / Benini, S.

Funding support

European Union, 1items

Citation

Journal: To Be Published
Title: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF N-terminal domain
Authors: Poonsiri, T. / Demitri, N. / Benini, S.

History

Deposition	Aug 9, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 14, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8kd8.cif.gz	81.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8kd8.ent.gz	59.2 KB	Display	PDB format
PDBx/mmJSON format	8kd8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8kd8_validation.pdf.gz	431.7 KB	Display	wwPDB validaton report
Full document	8kd8_full_validation.pdf.gz	432.2 KB	Display
Data in XML	8kd8_validation.xml.gz	8.9 KB	Display
Data in CIF	8kd8_validation.cif.gz	11.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kd/8kd8 ftp://data.pdbj.org/pub/pdb/validation_reports/kd/8kd8	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF

22.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF

defined by author&software
Evidence: gel filtration, MW calculated from the s200 16 60 standard curve is ~53.8 kDa, corresponding to dimer assembly.
44.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	62.200, 110.670, 69.474
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	N(5)-hydroxyornithine:cis-anhydromevalonyl coenzyme A-N(5)-transacylase sidF / Hydroxyornithine transacylase sidF / Siderophore biosynthesis protein F Mass: 22325.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (mold) Gene: sidF, AFUA_3G03400 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q4WF55, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

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

Mass: 22325.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (mold)
Gene: sidF, AFUA_3G03400 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4WF55, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.14 % / Description: Rod shape
Crystal grow	Temperature: 293 K / Method: batch mode Details: 0.2M potassium sodium tartrate tetrahydrate, 20% w/v polyethylene glycol 3350, cryoprotected with 40% Morpheus precipitant mix 3

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.58→29.438 Å / Num. obs: 7832 / % possible obs: 99.8 % / Redundancy: 12.2 % / B_iso Wilson estimate: 49.5 Å² / CC_1/2: 0.998 / Χ²: 0.97 / Net I/σ(I): 4.4
Reflection shell	Resolution: 2.58→2.7 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 4.4 / Num. unique obs: 927 / CC_1/2: 0.942 / Χ²: 0.8 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0415	refinement
XDS		data reduction
Aimless	0.7.9	data scaling
MrBUMP	2.2.6	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.581→29.438 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.934 / SU B: 8.651 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.402 / ESU R Free: 0.27
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.236	367	4.694 %	random
R_work	0.1726	7451	-	-
all	0.176	-	-	-
obs	-	7818	99.783 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 51.123 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.242 Å²	-0 Å²	-0 Å²
2-	-	1.351 Å²	0 Å²
3-	-	-	-1.109 Å²

Refinement step

Cycle: LAST / Resolution: 2.581→29.438 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1376	0	0	31	1407

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.012	1431
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	1298
X-RAY DIFFRACTION	r_angle_refined_deg	2.192	1.672	1967
X-RAY DIFFRACTION	r_angle_other_deg	0.834	1.58	2998
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.422	5	176
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	14.913	5	11
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.156	10	205
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.708	10	65
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	214
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	1719
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	331
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	261
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.178	0.2	1173
X-RAY DIFFRACTION	r_nbtor_refined	0.189	0.2	704
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	814
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	35
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.093	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.106	0.2	106
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.14	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	7.484	5.129	701
X-RAY DIFFRACTION	r_mcbond_other	7.485	5.132	701
X-RAY DIFFRACTION	r_mcangle_it	9.771	9.198	875
X-RAY DIFFRACTION	r_mcangle_other	9.785	9.207	876
X-RAY DIFFRACTION	r_scbond_it	9.052	5.58	730
X-RAY DIFFRACTION	r_scbond_other	9.046	5.589	731
X-RAY DIFFRACTION	r_scangle_it	11.835	9.942	1091
X-RAY DIFFRACTION	r_scangle_other	11.829	9.95	1092
X-RAY DIFFRACTION	r_lrange_it	13.927	53.179	1528
X-RAY DIFFRACTION	r_lrange_other	13.935	52.859	1527

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.581-2.647	0.358	36	0.242	513	0.25	557	0.93	0.972	98.5637	0.2
2.647-2.719	0.341	24	0.235	519	0.239	543	0.948	0.969	100	0.199
2.719-2.797	0.302	34	0.213	503	0.218	537	0.934	0.976	100	0.172
2.797-2.883	0.326	23	0.201	498	0.205	521	0.943	0.978	100	0.169
2.883-2.976	0.265	15	0.192	487	0.195	502	0.957	0.979	100	0.163
2.976-3.08	0.243	21	0.178	472	0.18	493	0.958	0.98	100	0.157
3.08-3.195	0.384	13	0.169	461	0.174	474	0.934	0.981	100	0.148
3.195-3.323	0.171	19	0.171	446	0.171	465	0.984	0.982	100	0.157
3.323-3.469	0.265	27	0.184	417	0.189	444	0.96	0.98	100	0.168
3.469-3.636	0.197	19	0.154	389	0.156	408	0.975	0.987	100	0.149
3.636-3.829	0.188	16	0.16	385	0.161	402	0.981	0.986	99.7512	0.156
3.829-4.057	0.317	24	0.184	370	0.192	395	0.936	0.98	99.7468	0.179
4.057-4.332	0.268	12	0.171	342	0.174	354	0.955	0.983	100	0.17
4.332-4.67	0.196	24	0.133	313	0.137	337	0.98	0.989	100	0.143
4.67-5.103	0.202	7	0.144	308	0.145	315	0.985	0.989	100	0.154
5.103-5.684	0.183	13	0.148	279	0.15	292	0.978	0.988	100	0.153
5.684-6.523	0.275	13	0.186	244	0.19	257	0.977	0.981	100	0.185
6.523-7.893	0.158	13	0.173	217	0.172	230	0.989	0.978	100	0.177
7.893-10.781	0.162	7	0.139	171	0.14	178	0.986	0.988	100	0.159
10.781-29.438	0.221	7	0.255	117	0.253	124	0.932	0.952	100	0.298

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