PDB-9kq9: The structure of the YcfA-GTP from Erwinia amylovora

ID or keywords:

Entry

Database: PDB / ID: 9kq9

Title

The structure of the YcfA-GTP from Erwinia amylovora

Components

Asparagine synthetase domain-containing protein

Keywords

BIOSYNTHETIC PROTEIN / adenylation / catalyze / tetradecamer / complex

Function / homology

Rossmann-like alpha/beta/alpha sandwich fold / 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: 2.59 Å

Authors

Zhang, L.

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	9kq9.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb9kq9.ent.gz	1003.3 KB	Display	PDB format
PDBx/mmJSON format	9kq9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kq9_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	9kq9_full_validation.pdf.gz	2.3 MB	Display
Data in XML	9kq9_validation.xml.gz	126.7 KB	Display
Data in CIF	9kq9_validation.cif.gz	164 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kq/9kq9 ftp://data.pdbj.org/pub/pdb/validation_reports/kq/9kq9	HTTPS FTP

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Related structure data

Related structure data	9kq4C 9kq6C 9kq7C 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

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

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

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

1

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

2

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

Unit cell

Length a, b, c (Å)	68.174, 134.366, 233.837
Angle α, β, γ (deg.)	90.00, 98.35, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	C-349- HOH
2	1	F-328- 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 Source: (gene. exp.) Erwinia amylovora ATCC 49946 (bacteria) Gene: BN437_1047 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A831ERP2
#2: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 664 / 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: 2.9 Å³/Da / Density % sol: 57.52 %
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: 2.59→47.51 Å / Num. obs: 128775 / % possible obs: 99.75 % / Redundancy: 6.8 % / CC_1/2: 0.993 / Net I/σ(I): 9.06
Reflection shell	Resolution: 2.594→2.661 Å / Num. unique obs: 12739 / CC_1/2: 0.608

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.59→47.51 Å / Cor.coef. F_o:F_c: 0.922 / Cor.coef. F_o:F_c free: 0.886 / SU B: 25.912 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.595 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25746	6531	5.1 %	RANDOM
R_work	0.21096	-	-	-
obs	0.21331	122219	99.79 %	-

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: 52.65 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.97 Å²	-0 Å²	0.24 Å²
2-	-	-0 Å²	0 Å²
3-	-	-	-1 Å²

Refinement step

Cycle: 1 / Resolution: 2.59→47.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24108	0	224	664	24996

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	24801
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	23550
X-RAY DIFFRACTION	r_angle_refined_deg	2.383	1.818	33612
X-RAY DIFFRACTION	r_angle_other_deg	0.784	1.75	54094
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.424	5	3044
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	12.884	5	154
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.468	10	4266
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	3818
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	28968
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5716
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	5.264	3.391	12224
X-RAY DIFFRACTION	r_mcbond_other	5.264	3.39	12224
X-RAY DIFFRACTION	r_mcangle_it	7.276	6.079	15252
X-RAY DIFFRACTION	r_mcangle_other	7.277	6.079	15253
X-RAY DIFFRACTION	r_scbond_it	6.339	3.81	12577
X-RAY DIFFRACTION	r_scbond_other	6.338	3.81	12577
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	8.811	6.857	18361
X-RAY DIFFRACTION	r_long_range_B_refined	10.328	37.89	28013
X-RAY DIFFRACTION	r_long_range_B_other	10.326	37.89	27882
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.594→2.661 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.321	480	-
R_work	0.277	8891	-
obs	-	-	98.75 %

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	0.8947	0.0978	0.0627	1.5328	0.276	0.6224	-0.0121	-0.0093	-0.1318	-0.0378	-0.0092	-0.0432	0.0208	0.0413	0.0214	0.0659	0.0043	0.0227	0.1356	-0.0067	0.0285	14.6465	1.3937	-42.9608
2	0.5535	0.3513	0.144	1.033	1.5057	2.5483	-0.0106	0.1248	0.2027	-0.1656	-0.0079	0.105	-0.2478	-0.056	0.0185	0.127	0.0044	0.0102	0.1807	0.058	0.0766	14.5165	27.3767	-9.2998
3	0.6278	0.274	-0.3967	0.5126	-0.4534	1.9215	-0.0091	0.0657	0.0558	-0.0109	-0.0096	-0.0243	-0.0858	-0.0568	0.0187	0.0894	-0.0147	-0.0123	0.118	0.0145	0.0128	13.6221	17.4317	30.856
4	0.5475	-0.1796	-0.3112	0.0907	-0.1353	2.4515	-0.0429	-0.0583	-0.1122	-0.02	-0.0237	0.0085	0.3237	0.0595	0.0666	0.2288	0.0228	0.0696	0.2996	0.0803	0.2351	14.464	-67.4251	-12.2712
5	0.3736	0.1351	0.1018	1.9119	1.074	0.949	-0.0017	-0.063	0.0164	0.203	0.0035	0.0784	0.1496	0.0315	-0.0019	0.1854	0.0399	0.0176	0.2639	-0.0105	0.1167	14.0559	-59.1578	29.6539
6	0.4383	-0.3381	0.038	1.609	-1.4838	1.606	-0.0339	0.0642	-0.1728	-0.1973	0.0042	0.0281	0.2593	-0.0587	0.0297	0.1623	0.0088	0.0477	0.2131	-0.0092	0.2505	14.363	-40.5627	-44.5208
7	0.5632	0.3284	0.3137	2.1226	-0.5956	0.5155	-0.0186	-0.0124	0.0109	0.1102	0.027	0.0935	-0.0126	-0.0258	-0.0083	0.105	0.0237	0.0131	0.1607	-0.0261	0.0776	14.0362	-21.3438	49.0504
8	1.3295	0.1056	-0.0527	1.6202	0.2264	0.5137	-0.0588	0.0344	0.2149	-0.0128	0.04	-0.0092	-0.1171	0.0481	0.0188	0.0501	-0.0173	-0.0121	0.1618	-0.0046	0.0393	43.3539	15.22	152.5448
9	1.0678	-0.0927	0.1887	0.7041	1.2122	2.237	-0.002	-0.1733	-0.2037	0.1743	-0.0216	0.0454	0.3142	-0.0127	0.0236	0.1163	0.0093	0.0495	0.2194	0.0584	0.0659	33.5686	-10.5419	120.4464
10	0.973	-0.2434	0.6961	0.3524	-0.5153	1.7844	-0.0382	-0.0862	-0.0691	0.0159	0.0365	0.0342	0.0544	-0.006	0.0018	0.0533	0.0307	0.0288	0.1333	0.0054	0.022	21.396	-0.3886	82.3299
11	0.5667	0.1626	0.8571	0.1981	-0.0054	2.797	-0.0049	0.0415	0.1066	0.0327	-0.1545	-0.0877	-0.2492	0.0495	0.1594	0.1565	-0.0155	0.052	0.3072	0.1024	0.3044	34.5353	84.04	122.9585
12	0.1081	0.2937	0.1128	1.915	0.9607	1.1367	-0.036	0.0791	0.0511	-0.2662	-0.0234	0.2041	-0.1261	-0.0854	0.0594	0.1936	0.0145	0.0311	0.2799	-0.0258	0.1773	21.8993	76.016	83.2718
13	0.8099	-0.0777	-0.0198	1.727	-1.1188	0.7332	-0.0364	-0.0718	0.2996	0.2616	-0.0046	-0.1222	-0.1865	0.0082	0.041	0.2394	-0.0215	-0.0241	0.2748	0.031	0.3837	43.8298	57.2965	154.0739
14	0.4715	-0.2495	-0.1693	2.2595	-0.3482	0.8425	0.0287	0.0159	0.0491	-0.1802	0.0069	0.1669	-0.0255	-0.0723	-0.0356	0.1521	-0.0126	0.0103	0.1703	-0.0189	0.0961	16.5261	38.2928	64.7288

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 223
2	X-RAY DIFFRACTION	2	C	6 - 226
3	X-RAY DIFFRACTION	3	E	7 - 301
4	X-RAY DIFFRACTION	4	F	7 - 226
5	X-RAY DIFFRACTION	5	H	7 - 301
6	X-RAY DIFFRACTION	6	L	6 - 301
7	X-RAY DIFFRACTION	7	N	6 - 301
8	X-RAY DIFFRACTION	8	B	7 - 226
9	X-RAY DIFFRACTION	9	D	7 - 226
10	X-RAY DIFFRACTION	10	G	7 - 301
11	X-RAY DIFFRACTION	11	I	7 - 226
12	X-RAY DIFFRACTION	12	J	7 - 301
13	X-RAY DIFFRACTION	13	K	6 - 224
14	X-RAY DIFFRACTION	14	M	6 - 301

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