PDB-9kq7: The structure of the YcfA from Erwinia amylovora bound with ATP

ID or keywords:

Entry

Database: PDB / ID: 9kq7

Title

The structure of the YcfA from Erwinia amylovora bound with ATP

Components

Asparagine synthetase domain-containing protein

Keywords

BIOSYNTHETIC PROTEIN / tetradecamer / YcfA-YcfC bipartite enzyme system / 6-Thioguanine biosynthesis

Function / homology

Rossmann-like alpha/beta/alpha sandwich fold / ADENOSINE-5'-TRIPHOSPHATE / Asparagine synthetase domain-containing protein

Function and homology information

Biological species

Erwinia amylovora ATCC 49946 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.84 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	9kq7.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb9kq7.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	9kq7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kq7_validation.pdf.gz	5.2 MB	Display	wwPDB validaton report
Full document	9kq7_full_validation.pdf.gz	5.3 MB	Display
Data in XML	9kq7_validation.xml.gz	121.1 KB	Display
Data in CIF	9kq7_validation.cif.gz	155.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kq/9kq7 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/9kq7	HTTPS FTP

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Related structure data

Related structure data	9kq4C 9kq6C 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

B: Asparagine synthetase domain-containing protein

E: Asparagine synthetase domain-containing protein

G: Asparagine synthetase domain-containing protein

I: Asparagine synthetase domain-containing protein

J: Asparagine synthetase domain-containing protein

L: Asparagine synthetase domain-containing protein

M: Asparagine synthetase domain-containing protein

A: Asparagine synthetase domain-containing protein

C: Asparagine synthetase domain-containing protein

D: Asparagine synthetase domain-containing protein

F: Asparagine synthetase domain-containing protein

H: Asparagine synthetase domain-containing protein

K: Asparagine synthetase domain-containing protein

N: Asparagine synthetase domain-containing protein

hetero molecules

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

1

B: Asparagine synthetase domain-containing protein

E: Asparagine synthetase domain-containing protein

G: Asparagine synthetase domain-containing protein

I: Asparagine synthetase domain-containing protein

J: Asparagine synthetase domain-containing protein

L: Asparagine synthetase domain-containing protein

M: Asparagine synthetase domain-containing protein

hetero molecules

B: Asparagine synthetase domain-containing protein

E: Asparagine synthetase domain-containing protein

G: Asparagine synthetase domain-containing protein

I: Asparagine synthetase domain-containing protein

J: Asparagine synthetase domain-containing protein

L: Asparagine synthetase domain-containing protein

M: Asparagine synthetase domain-containing protein

hetero molecules

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

2

A: Asparagine synthetase domain-containing protein

C: Asparagine synthetase domain-containing protein

D: Asparagine synthetase domain-containing protein

F: Asparagine synthetase domain-containing protein

H: Asparagine synthetase domain-containing protein

K: Asparagine synthetase domain-containing protein

N: Asparagine synthetase domain-containing protein

hetero molecules

A: Asparagine synthetase domain-containing protein

C: Asparagine synthetase domain-containing protein

D: Asparagine synthetase domain-containing protein

F: Asparagine synthetase domain-containing protein

H: Asparagine synthetase domain-containing protein

K: Asparagine synthetase domain-containing protein

N: Asparagine synthetase domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.710, 134.330, 235.960
Angle α, β, γ (deg.)	90.00, 98.43, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	H-409- 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: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 58.81 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium malonate pH 7.0 and 20% 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: 2.84→33.34 Å / Num. obs: 101379 / % possible obs: 99.82 % / Redundancy: 2 % / CC_1/2: 0.996 / Net I/σ(I): 11.32
Reflection shell	Resolution: 2.84→2.913 Å / Num. unique obs: 10114 / CC_1/2: 0.542

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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: 2.84→33.34 Å / Cor.coef. F_o:F_c: 0.929 / Cor.coef. F_o:F_c free: 0.901 / SU B: 39.944 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25248	5003	4.9 %	RANDOM
R_work	0.20965	-	-	-
obs	0.21178	96376	99.84 %	-

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: 68.329 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.27 Å²	0 Å²	-0.59 Å²
2-	-	-1.54 Å²	-0 Å²
3-	-	-	-1.49 Å²

Refinement step

Cycle: 1 / Resolution: 2.84→33.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24127	0	434	223	24784

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	25066
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	23633
X-RAY DIFFRACTION	r_angle_refined_deg	2.307	1.815	34013
X-RAY DIFFRACTION	r_angle_other_deg	0.747	1.749	54294
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.641	5	3050
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	13.763	5	154
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.924	10	4282
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	3871
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	29072
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5758
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	5.304	3.306	12242
X-RAY DIFFRACTION	r_mcbond_other	5.302	3.306	12242
X-RAY DIFFRACTION	r_mcangle_it	8.068	5.929	15278
X-RAY DIFFRACTION	r_mcangle_other	8.068	5.929	15279
X-RAY DIFFRACTION	r_scbond_it	6.038	3.701	12824
X-RAY DIFFRACTION	r_scbond_other	6.038	3.701	12824
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	9.03	6.682	18736
X-RAY DIFFRACTION	r_long_range_B_refined	11.343	35.15	28026
X-RAY DIFFRACTION	r_long_range_B_other	11.343	35.15	28011
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.84→2.913 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.385	387	-
R_work	0.35	7114	-
obs	-	-	99.96 %

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	2.4234	-1.0625	1.1925	0.8615	-1.0622	1.4769	0.0238	-0.1251	-0.0233	0.0555	0.024	0.0296	0.1428	0.0475	-0.0478	0.4638	0.0364	0.0377	0.4334	-0.0394	0.018	-30.1589	1.3608	-33.7126
2	0.8774	-0.8701	-0.0243	3.2272	-0.3235	0.0573	-0.0022	0.3163	-0.0031	-0.5591	0.021	0.1939	0.0439	-0.0347	-0.0188	0.6073	-0.1029	0.0728	0.669	-0.0253	0.3307	-35.3039	39.8828	-50.8789
3	0.2068	-0.2321	-0.452	1.6117	1.022	1.3158	-0.0169	0.1705	0.0037	-0.4013	-0.1046	0.1088	-0.1514	-0.1015	0.1215	0.5488	-0.0715	-0.0371	0.6156	0.0369	0.5041	-30.0044	77.0952	-32.1956
4	1.9807	0.8496	0.1776	2.3567	0.0102	0.787	0.0122	0.1548	0.2954	0.0466	-0.1431	0.1494	-0.0935	-0.0246	0.1309	0.3533	0.028	0.0034	0.4403	0.0534	0.0626	-8.5222	16.1792	36.8542
5	0.8789	0.5922	0.9828	0.9009	1.2697	1.8522	0.1086	-0.1917	-0.3273	0.3153	-0.0268	0.0245	0.3963	-0.001	-0.0818	0.4874	0.0494	0.0929	0.5498	0.0592	0.2505	-18.3122	-9.3633	4.78
6	0.1162	0.1776	-0.0984	2.1125	-1.1257	0.6026	-0.049	-0.087	0.2291	0.4426	0.0399	-0.0453	-0.2637	-0.0045	0.0091	0.5533	0.0084	-0.0961	0.6378	0.0287	0.6902	-7.9376	58.0596	38.3219
7	0.6438	0.1909	0.1501	0.0753	-0.0629	3.1251	-0.0768	0.0396	0.0248	0.0131	-0.0715	-0.0227	-0.382	-0.0819	0.1483	0.441	-0.0193	-0.1071	0.529	0.0968	0.5253	-17.5435	84.9579	6.9289
8	0.4541	-0.5574	0.2578	2.4125	-1.4397	0.8845	-0.0442	0.1003	-0.3138	-0.4641	0.0462	0.0871	0.3079	-0.1098	-0.002	0.347	-0.03	0.1753	0.4104	0.0047	0.31	-38.0347	-40.5797	-161.2819
9	2.1354	-0.8981	0.1498	2.2828	0.591	1.3914	-0.0334	-0.0147	-0.0893	-0.1422	-0.0968	0.0716	0.025	0.0134	0.1301	0.1425	-0.0316	0.0354	0.2814	0.0337	0.0301	-38.0648	1.2205	-159.6638
10	0.9232	-0.2483	-0.7169	1.1258	1.5454	2.3393	0.1135	0.2389	0.2713	-0.2677	-0.0767	0.1041	-0.3055	-0.2014	-0.0368	0.2221	-0.0322	-0.0734	0.294	0.0468	0.1656	-37.9949	26.8424	-126.133
11	0.1933	0.4591	0.5113	1.5932	1.2606	1.3893	0.043	-0.0778	0.0197	0.3663	-0.0783	0.1264	0.1749	-0.1052	0.0353	0.2439	0.0805	0.0662	0.424	0.0026	0.2873	-37.9919	-59.4906	-87.5362
12	0.8981	-0.1204	0.7918	0.2973	-0.0697	3.3308	0.0242	-0.1008	-0.0591	0.0829	-0.0028	-0.0038	0.3751	-0.1806	-0.0214	0.225	0.0278	0.1399	0.2974	0.0694	0.3065	-38.011	-67.5726	-128.8179
13	0.7739	0.4808	-0.1759	3.2518	-0.6041	0.1238	-0.0556	-0.3532	0.0791	0.5541	0.0779	0.1148	-0.0835	0.0157	-0.0224	0.3437	0.0685	-0.0625	0.5148	-0.0447	0.2207	-38.029	-22.3723	-67.9484
14	0.9456	0.7453	-1.0363	0.8618	-1.2094	1.7215	0.077	0.0697	0.0333	0.0659	-0.0098	0.0622	-0.1462	-0.0264	-0.0672	0.2338	-0.0445	-0.0813	0.2869	0.007	0.0376	-37.9614	16.177	-85.9654

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	8 - 301
2	X-RAY DIFFRACTION	2	E	6 - 301
3	X-RAY DIFFRACTION	3	G	8 - 301
4	X-RAY DIFFRACTION	4	I	6 - 301
5	X-RAY DIFFRACTION	5	J	7 - 301
6	X-RAY DIFFRACTION	6	L	8 - 301
7	X-RAY DIFFRACTION	7	M	6 - 301
8	X-RAY DIFFRACTION	8	A	8 - 301
9	X-RAY DIFFRACTION	9	C	6 - 301
10	X-RAY DIFFRACTION	10	D	7 - 301
11	X-RAY DIFFRACTION	11	F	6 - 301
12	X-RAY DIFFRACTION	12	H	7 - 301
13	X-RAY DIFFRACTION	13	K	8 - 301
14	X-RAY DIFFRACTION	14	N	6 - 301

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