PDB-9kqd: YcfA-D19A-ATP-GTP complex

ID or keywords:

Entry

Database: PDB / ID: 9kqd

Title

YcfA-D19A-ATP-GTP complex

Components

Asparagine synthetase domain-containing protein

Keywords

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

Function / homology

Rossmann-like alpha/beta/alpha sandwich fold / ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-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: 2.1 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. / Yan, W. / Chen, P. / Jia, X. / Zhang, N. / Zhou, D. / Long, Z. / Zhang, L. / Zhu, X. / Cheng, W.

History

Deposition	Nov 25, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Oct 1, 2025	Provider: repository / Type: Initial release
Revision 1.1	Oct 22, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9kqd.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb9kqd.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	9kqd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kq/9kqd ftp://data.pdbj.org/pub/pdb/validation_reports/kq/9kqd	HTTPS FTP

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Related structure data

Related structure data	9kq4C 9kq6C 9kq7C 9kq9C 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

D: Asparagine synthetase domain-containing protein

G: Asparagine synthetase domain-containing protein

I: Asparagine synthetase domain-containing protein

J: Asparagine synthetase domain-containing protein

K: Asparagine synthetase domain-containing protein

M: Asparagine synthetase domain-containing protein

A: Asparagine synthetase domain-containing protein

C: Asparagine synthetase domain-containing protein

E: Asparagine synthetase domain-containing protein

F: Asparagine synthetase domain-containing protein

H: Asparagine synthetase domain-containing protein

L: Asparagine synthetase domain-containing protein

N: Asparagine synthetase domain-containing protein

hetero molecules

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

1

B: Asparagine synthetase domain-containing protein

D: Asparagine synthetase domain-containing protein

G: Asparagine synthetase domain-containing protein

I: Asparagine synthetase domain-containing protein

J: Asparagine synthetase domain-containing protein

K: Asparagine synthetase domain-containing protein

M: Asparagine synthetase domain-containing protein

hetero molecules

B: Asparagine synthetase domain-containing protein

D: Asparagine synthetase domain-containing protein

G: Asparagine synthetase domain-containing protein

I: Asparagine synthetase domain-containing protein

J: Asparagine synthetase domain-containing protein

K: Asparagine synthetase domain-containing protein

M: Asparagine synthetase domain-containing protein

hetero molecules

defined by author&software
Evidence: microscopy
381 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

E: Asparagine synthetase domain-containing protein

F: Asparagine synthetase domain-containing protein

H: Asparagine synthetase domain-containing protein

L: 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

E: Asparagine synthetase domain-containing protein

F: Asparagine synthetase domain-containing protein

H: Asparagine synthetase domain-containing protein

L: Asparagine synthetase domain-containing protein

N: Asparagine synthetase domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.163, 135.089, 234.795
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	K-545- HOH
2	1	E-554- HOH

#1: Protein	Asparagine synthetase domain-containing protein Mass: 26137.902 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Details: Sequence reference for Erwinia amylovora (strain ATCC 49946) (716540) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A831ERP2. 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: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2451 / 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: 3.22 Å³/Da / Density % sol: 61.8 %
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: 0.979 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: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.1→48.89 Å / Num. obs: 268269 / % possible obs: 99.35 % / Redundancy: 5 % / CC_1/2: 0.999 / Net I/σ(I): 16.53
Reflection shell	Resolution: 2.1→2.151 Å / Num. unique obs: 25828 / CC_1/2: 0.692

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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: 2.1→48.89 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.955 / SU B: 7.591 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19226	13266	4.9 %	RANDOM
R_work	0.16595	-	-	-
obs	0.16725	255003	99.15 %	-

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: 38.465 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.7 Å²	0 Å²	0.19 Å²
2-	-	0.26 Å²	-0 Å²
3-	-	-	-0.96 Å²

Refinement step

Cycle: 1 / Resolution: 2.1→48.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24281	0	896	2451	27628

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	25708
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	23995
X-RAY DIFFRACTION	r_angle_refined_deg	2.238	1.823	35016
X-RAY DIFFRACTION	r_angle_other_deg	0.727	1.747	55140
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.272	5	3077
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	15.772	5	154
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.52	10	4282
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	4006
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	29516
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5834
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	2.347	1.991	12353
X-RAY DIFFRACTION	r_mcbond_other	2.346	1.991	12353
X-RAY DIFFRACTION	r_mcangle_it	3.13	3.555	15415
X-RAY DIFFRACTION	r_mcangle_other	3.13	3.555	15416
X-RAY DIFFRACTION	r_scbond_it	4.744	2.487	13355
X-RAY DIFFRACTION	r_scbond_other	4.744	2.487	13355
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.341	4.433	19602
X-RAY DIFFRACTION	r_long_range_B_refined	8.894	28.2	30402
X-RAY DIFFRACTION	r_long_range_B_other	8.831	26.18	29705
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.151 Å

	R_factor	Num. reflection	% reflection
R_free	0.293	965	-
R_work	0.266	17373	-
obs	-	-	92.16 %

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	0.5268	0.348	0.5778	0.6045	1.0079	1.8551	-0.0581	0.1048	0.1742	-0.1296	-0.0861	0.1483	-0.2338	-0.0363	0.1442	0.1783	0.0342	0.0028	0.1821	-0.1193	0.3307	12.0431	-169.0605	211.4433
2	0.6856	-0.0967	0.1182	1.5893	0.9646	1.0332	0.0082	-0.0884	0.172	-0.0647	-0.0093	0.0607	-0.1142	-0.0055	0.0011	0.0594	0.0103	-0.0178	0.1236	-0.0791	0.1032	5.4214	-207.5737	195.939
3	0.4725	-0.4404	0.2936	1.9209	-0.8483	1.0291	0.0442	0.0148	-0.0795	-0.0845	-0.0047	0.0154	0.169	-0.1585	-0.0395	0.1615	-0.0757	-0.0176	0.1999	-0.0057	0.0676	12.4993	-245.064	213.6126
4	0.5441	-0.2237	-0.0199	2.684	-0.4804	0.5447	-0.024	-0.1069	0.132	0.2199	0.0292	-0.1692	-0.1794	0.0615	-0.0052	0.1673	0.0262	0.0092	0.1318	0.0571	0.1403	40.5284	-184.2186	279.9135
5	1.2901	0.4116	0.4951	1.2547	0.5929	1.577	0.019	0.0977	-0.0427	-0.0238	0.0085	-0.031	0.1122	0.0583	-0.0276	0.0682	-0.0042	-0.0001	0.0492	0.0209	0.0163	41.1747	-226.2391	280.6938
6	0.6397	-0.3789	0.1422	1.0991	-0.7608	1.6311	-0.0839	-0.0984	-0.0567	0.0687	-0.046	-0.1171	-0.1654	0.0239	0.1299	0.1712	0.0217	0.0015	0.0698	-0.0134	0.1776	27.7162	-158.6423	249.0916
7	0.7258	0.2067	0.8215	0.2975	-0.2581	2.0453	0.0287	0.0777	-0.1055	-0.124	-0.0256	-0.0534	0.377	0.0733	-0.0031	0.2933	-0.0244	0.0047	0.1764	-0.0351	0.1364	28.9468	-254.1021	251.6979
8	1.2873	-0.4139	-0.5333	1.2621	0.6764	1.6655	0.0197	-0.1096	0.0545	0.0048	0.0161	-0.0366	-0.1046	0.0599	-0.0358	0.0751	-0.0035	-0.0267	0.0478	0.0174	0.027	-70.0677	-94.0377	306.2975
9	0.3931	0.0954	0.0324	2.5764	-0.5841	0.5444	-0.0469	0.1219	-0.1327	-0.2119	0.0483	-0.1839	0.1899	0.0667	-0.0014	0.168	-0.0277	-0.0374	0.1356	0.0464	0.1575	-70.6365	-136.1019	307.0762
10	0.6641	0.3867	-0.2311	1.1734	-0.68	1.739	-0.0878	0.1003	0.0515	-0.0712	-0.0524	-0.1056	0.152	0.0035	0.1401	0.1656	-0.0256	-0.0305	0.0703	-0.0189	0.1726	-83.6258	-161.517	337.8309
11	0.4926	0.4849	-0.2809	1.7511	-0.8768	0.9569	0.0474	-0.0328	0.0867	0.0782	-0.02	0.01	-0.1811	-0.1551	-0.0273	0.1723	0.0778	-0.0131	0.1983	-0.002	0.0722	-98.6903	-75.1601	373.4052
12	0.7561	0.0716	-0.1432	1.6821	0.9849	1.062	0.0009	0.0975	-0.1847	0.0662	-0.0097	0.0565	0.1143	-0.0075	0.0088	0.0547	-0.0085	-0.0153	0.1205	-0.0767	0.1001	-105.8359	-112.7265	390.9789
13	0.6848	-0.2198	-0.827	0.2587	-0.1795	2.0922	0.0291	-0.0589	0.0874	0.1205	-0.0057	-0.0502	-0.3912	0.0436	-0.0234	0.295	0.0207	-0.0297	0.1727	-0.0252	0.133	-82.4994	-66.3682	335.2585
14	0.53	-0.3978	-0.6644	0.7152	1.0764	2.0458	-0.068	-0.0965	-0.1751	0.1424	-0.0788	0.163	0.2461	-0.0406	0.1469	0.1732	-0.0456	-0.028	0.1768	-0.1252	0.3253	-99.1862	-151.2046	375.5521

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	6 - 302
2	X-RAY DIFFRACTION	2	D	7 - 302
3	X-RAY DIFFRACTION	3	G	6 - 302
4	X-RAY DIFFRACTION	4	I	6 - 302
5	X-RAY DIFFRACTION	5	J	6 - 302
6	X-RAY DIFFRACTION	6	K	6 - 302
7	X-RAY DIFFRACTION	7	M	6 - 302
8	X-RAY DIFFRACTION	8	A	6 - 302
9	X-RAY DIFFRACTION	9	C	7 - 302
10	X-RAY DIFFRACTION	10	E	5 - 302
11	X-RAY DIFFRACTION	11	F	7 - 302
12	X-RAY DIFFRACTION	12	H	6 - 302
13	X-RAY DIFFRACTION	13	L	6 - 302
14	X-RAY DIFFRACTION	14	N	6 - 302

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