PDB-9kq6: The structure of the apo-YcfA from Erwinia amylovora

ID or keywords:

Entry

Database: PDB / ID: 9kq6

Title

The structure of the apo-YcfA from Erwinia amylovora

Components

Asparagine synthetase domain-containing protein

Keywords

BIOSYNTHETIC PROTEIN / YcfA-YcfC bipartite enzyme system / adenylation activity / L-Cys addition / tetradecamer / 6-Thioguanine biosynthesis

Function / homology

Rossmann-like alpha/beta/alpha sandwich fold / Asparagine synthetase domain-containing protein

Function and homology information

Biological species

Erwinia amylovora ATCC 49946 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.34 Å

Authors

Zhang, L. / Dou, C. / Zheng, Y.H. / Zhu, X.F. / Cheng, W.

Funding support

China, 2items

Citation

Journal: Nat Commun / Year: 2025
Title: The Mechanism of Thioamide Formation by the YcfA-YcfC System in 6-Thioguanine Biosynthesis
Authors: Zhang, L. / Dou, C. / Zheng, Y.H. / Zhu, X.F. / Cheng, W.

History

Deposition	Nov 25, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Oct 1, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9kq6.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb9kq6.ent.gz	996.6 KB	Display	PDB format
PDBx/mmJSON format	9kq6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kq6_validation.pdf.gz	522.2 KB	Display	wwPDB validaton report
Full document	9kq6_full_validation.pdf.gz	574.2 KB	Display
Data in XML	9kq6_validation.xml.gz	119.6 KB	Display
Data in CIF	9kq6_validation.cif.gz	158.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kq/9kq6 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/9kq6	HTTPS FTP

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Related structure data

Related structure data	9kq4C 9kq7C 9kq9C 9kqdC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

N: Asparagine synthetase domain-containing protein

H: Asparagine synthetase domain-containing protein

D: Asparagine synthetase domain-containing protein

C: Asparagine synthetase domain-containing protein

L: Asparagine synthetase domain-containing protein

A: Asparagine synthetase domain-containing protein

M: Asparagine synthetase domain-containing protein

J: Asparagine synthetase domain-containing protein

F: Asparagine synthetase domain-containing protein

K: Asparagine synthetase domain-containing protein

E: Asparagine synthetase domain-containing protein

I: Asparagine synthetase domain-containing protein

B: Asparagine synthetase domain-containing protein

G: Asparagine synthetase domain-containing protein

366 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

N: Asparagine synthetase domain-containing protein

H: Asparagine synthetase domain-containing protein

C: Asparagine synthetase domain-containing protein

L: Asparagine synthetase domain-containing protein

A: Asparagine synthetase domain-containing protein

F: Asparagine synthetase domain-containing protein

E: Asparagine synthetase domain-containing protein

N: Asparagine synthetase domain-containing protein

H: Asparagine synthetase domain-containing protein

C: Asparagine synthetase domain-containing protein

L: Asparagine synthetase domain-containing protein

A: Asparagine synthetase domain-containing protein

F: Asparagine synthetase domain-containing protein

E: Asparagine synthetase domain-containing protein

defined by author&software
Evidence: microscopy
366 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Asparagine synthetase domain-containing protein

M: Asparagine synthetase domain-containing protein

J: Asparagine synthetase domain-containing protein

K: Asparagine synthetase domain-containing protein

I: Asparagine synthetase domain-containing protein

B: Asparagine synthetase domain-containing protein

G: Asparagine synthetase domain-containing protein

D: Asparagine synthetase domain-containing protein

M: Asparagine synthetase domain-containing protein

J: Asparagine synthetase domain-containing protein

K: Asparagine synthetase domain-containing protein

I: Asparagine synthetase domain-containing protein

B: Asparagine synthetase domain-containing protein

G: Asparagine synthetase domain-containing protein

defined by author&software
366 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	69.758, 134.923, 234.270
Angle α, β, γ (deg.)	90.00, 98.55, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	C-325- HOH
2	1	C-329- HOH

#1: Protein	Asparagine synthetase domain-containing protein / YcfA Mass: 26137.902 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Details: The sequence of organism Erwinia amylovora ATCC 49946 is not available during the biocuration, replaced by A0A831ERP2 temporarily. Source: (gene. exp.) Erwinia amylovora ATCC 49946 (bacteria) Gene: BN437_1047 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A831ERP2
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 395 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.93 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 3.5% Tacsimate and 25% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2.34→48.28 Å / Num. obs: 178211 / % possible obs: 99.25 % / Redundancy: 4.1 % / CC_1/2: 0.996 / Net I/σ(I): 10.97
Reflection shell	Resolution: 2.345→2.406 Å / Num. unique obs: 16975 / CC_1/2: 0.463

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.34→48.28 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.894 / SU B: 26.861 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2847	9081	5.1 %	RANDOM
R_work	0.24655	-	-	-
obs	0.24847	169107	99.28 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 53.473 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.47 Å²	-0 Å²	0.53 Å²
2-	-	-0.8 Å²	-0 Å²
3-	-	-	-0.79 Å²

Refinement step

Cycle: 1 / Resolution: 2.34→48.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24341	0	0	395	24736

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	24835
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	23701
X-RAY DIFFRACTION	r_angle_refined_deg	2.066	1.813	33615
X-RAY DIFFRACTION	r_angle_other_deg	0.681	1.748	54442
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.037	5	3079
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.185	5	153
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.274	10	4302
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	3810
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	29154
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5746
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.128	2.283	12358
X-RAY DIFFRACTION	r_mcbond_other	3.127	2.283	12358
X-RAY DIFFRACTION	r_mcangle_it	4.839	4.089	15423
X-RAY DIFFRACTION	r_mcangle_other	4.839	4.09	15424
X-RAY DIFFRACTION	r_scbond_it	3.403	2.575	12477
X-RAY DIFFRACTION	r_scbond_other	3.403	2.575	12478
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.235	4.625	18193
X-RAY DIFFRACTION	r_long_range_B_refined	7.705	24.84	27728
X-RAY DIFFRACTION	r_long_range_B_other	7.705	24.81	27715
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.345→2.406 Å

	Num. reflection	% reflection
R_free	629	-
R_work	11785	-
obs	-	93.55 %

Refinement TLS params.

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

ID	L11 (°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)
1	0.7292	0.1915	0.2145	2.6213	-0.6611	0.6579	-0.0006	0.0166	-0.0531	0.0539	0.0321	0.0564	0.0053	-0.0332	-0.0316	0.4759	0.0444	-0.0316	0.1751	-0.0105	0.1059	14.728	-14.284	48.73
2	0.6652	0.33	0.0637	1.486	0.8889	0.9198	-0.01	-0.0939	-0.0486	0.0901	-0.0027	0.0286	0.0742	-0.0137	0.0127	0.5179	0.0493	-0.0385	0.2962	-0.0479	0.2219	14.428	-52.209	29.348
3	0.8232	0.3026	0.5994	0.8676	0.792	1.0707	0.0511	-0.2164	-0.2155	0.1081	-0.0837	0.0841	0.1842	0.0059	0.0326	0.5945	0.0417	0.0344	0.3068	0.043	0.1524	34.035	-3.851	120.234
4	0.6359	0.146	-0.1881	0.8933	1.1679	1.8835	-0.004	0.2647	0.2357	-0.1158	-0.0125	0.1462	-0.1141	-0.0604	0.0166	0.4894	-0.0286	-0.0642	0.2503	0.0524	0.1241	14.662	34.793	-9.322
5	0.4117	-0.1646	-0.1816	1.6564	-1.1793	1.0983	-0.0322	0.0477	-0.2358	-0.1441	-0.0159	0.0548	0.1588	-0.0561	0.0481	0.5233	-0.0144	0.0425	0.2534	0.0003	0.3873	14.669	-33.094	-44.481
6	1.4511	-0.5957	-0.1541	1.7092	0.1669	0.674	-0.0199	-0.0291	-0.1507	-0.0398	-0.0028	0.0285	0.0135	0.0079	0.0228	0.4731	-0.031	-0.0041	0.1498	-0.0092	0.0287	14.754	9.07	-42.819
7	0.6817	-0.237	0.0441	2.5504	-0.4251	0.8079	-0.0254	-0.0511	0.0857	-0.049	0.0048	0.1275	-0.0052	-0.0204	0.0206	0.4938	0.0072	0.0149	0.2132	-0.006	0.1462	16.969	45.625	64.724
8	0.4851	-0.1075	-0.0772	1.3025	0.8848	0.8016	-0.0413	0.0539	0.0313	-0.1357	-0.003	0.1193	-0.0724	-0.0472	0.0443	0.5707	0.002	-0.0337	0.3815	-0.0318	0.269	22.397	83.201	83.487
9	0.5017	-0.3613	-0.0237	0.4285	0.2643	2.4031	-0.0228	-0.1021	-0.0434	0.0157	-0.0376	0.0649	0.1489	-0.1049	0.0603	0.5013	-0.0013	0.004	0.2926	0.0852	0.28	14.507	-60.248	-12.16
10	0.2752	-0.036	0.1124	1.2463	-0.97	0.7879	-0.0869	-0.0823	0.2927	0.1195	0.0251	0.0011	-0.1353	-0.086	0.0618	0.5697	-0.0344	-0.0219	0.3533	0.0285	0.4711	44.558	64.196	154.368
11	1.0172	0.1601	-0.9268	0.8244	-0.664	1.913	0.0024	0.0214	0.0544	-0.0404	-0.0188	0.0326	-0.0387	-0.0109	0.0164	0.4564	-0.0232	-0.0938	0.1534	0.0229	0.0313	14.005	24.479	30.897
12	0.9473	0.1986	0.7903	0.4751	0.4432	2.3738	-0.0413	0.0409	0.0946	0.0426	-0.1205	-0.0503	-0.1441	-0.0786	0.1618	0.5113	-0.0278	-0.0384	0.3353	0.113	0.2981	34.864	91.334	123.113
13	1.392	0.7266	0.084	1.9417	0.1762	0.4763	-0.0036	0.0663	0.245	-0.0536	-0.0408	0.0546	-0.0408	0.0237	0.0444	0.5182	-0.0171	-0.0091	0.2421	0.022	0.0616	44.018	22.266	152.575
14	1.3731	-0.4972	0.8815	0.7451	-0.4674	1.5029	0.0241	-0.0158	0.0007	0.0071	-0.0529	-0.0686	0.0917	0.0808	0.0288	0.5442	0.055	0.0286	0.1938	0.0141	0.0101	22.044	6.847	82.272

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	N	5 - 226
2	X-RAY DIFFRACTION	2	H	6 - 229
3	X-RAY DIFFRACTION	3	D	7 - 228
4	X-RAY DIFFRACTION	4	C	5 - 226
5	X-RAY DIFFRACTION	5	L	5 - 225
6	X-RAY DIFFRACTION	6	A	6 - 227
7	X-RAY DIFFRACTION	7	M	6 - 226
8	X-RAY DIFFRACTION	8	J	7 - 227
9	X-RAY DIFFRACTION	9	F	6 - 226
10	X-RAY DIFFRACTION	10	K	6 - 226
11	X-RAY DIFFRACTION	11	E	7 - 221
12	X-RAY DIFFRACTION	12	I	7 - 226
13	X-RAY DIFFRACTION	13	B	7 - 226
14	X-RAY DIFFRACTION	14	G	5 - 222

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