PDB-9vlx: Directional amination enzyme

ID or keywords:

Entry

Database: PDB / ID: 9vlx

Title

Directional amination enzyme

Components

Directional amination enzyme

Keywords

TRANSFERASE / transaminase / directional amination enzyme

Function / homology

: / PYRIDOXAL-5'-PHOSPHATE / Chem-PLR

Function and homology information

Biological species

Aspergillus fumigatus (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.99 Å

Authors

Cheng, F. / Xue, Y.P. / Zheng, Y.G.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Directional amination enzyme
Authors: Cheng, F. / Xue, Y.P. / Zheng, Y.G.

History

Deposition	Jun 26, 2025	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jul 1, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9vlx.cif.gz	265.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9vlx.ent.gz		Display	PDB format
PDBx/mmJSON format	9vlx.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/vl/9vlx ftp://data.pdbj.org/pub/pdb/validation_reports/vl/9vlx	HTTPS FTP

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Related structure data

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: Directional amination enzyme

B: Directional amination enzyme

hetero molecules

73.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Directional amination enzyme

B: Directional amination enzyme

hetero molecules

A: Directional amination enzyme

B: Directional amination enzyme

hetero molecules

defined by author&software
148 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	62.354, 96.998, 119.951
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Directional amination enzyme Mass: 36179.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (mold) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 258 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-A1ETM / 1-piperidin-1-yl-4-[2,4,5-tris(fluoranyl)phenyl]butane-1,3-dione Mass: 299.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₁₆F₃NO₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE Mass: 233.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₂NO₅P
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.54 Å³/Da / Density % sol: 51.59 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene Glycol 3350, Additive(PLP,5mM Ketone) PH range: 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 26, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.99→48.5 Å / Num. obs: 50475 / % possible obs: 99.38 % / Redundancy: 12.4 % / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.1285 / R_pim(I) all: 0.03777 / Net I/σ(I): 11.17
Reflection shell	Resolution: 1.99→2.061 Å / Redundancy: 9.2 % / R_merge(I) obs: 0.9933 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 4940 / CC_1/2: 0.852 / CC star: 0.959 / R_pim(I) all: 0.3388 / % possible all: 98.82

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS	INTEL64_Linux_x86_64	data reduction
pointless	1.12.16	data scaling
Coot	0.9.8	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.99→48.5 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2774	2432	4.83 %
R_work	0.2351	-	-
obs	0.2372	50323	99.29 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.99→48.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5036	0	98	249	5383

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5263
X-RAY DIFFRACTION	f_angle_d	0.876	7137
X-RAY DIFFRACTION	f_dihedral_angle_d	13.544	1951
X-RAY DIFFRACTION	f_chiral_restr	0.058	763
X-RAY DIFFRACTION	f_plane_restr	0.009	910

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.99-2.03	0.3394	132	0.3075	2759	X-RAY DIFFRACTION	98
2.03-2.07	0.3025	143	0.2642	2764	X-RAY DIFFRACTION	99
2.07-2.12	0.2656	154	0.2542	2745	X-RAY DIFFRACTION	100
2.12-2.18	0.28	133	0.2453	2800	X-RAY DIFFRACTION	99
2.18-2.23	0.2775	133	0.231	2792	X-RAY DIFFRACTION	99
2.23-2.3	0.2918	149	0.2263	2798	X-RAY DIFFRACTION	100
2.3-2.38	0.2432	111	0.2309	2807	X-RAY DIFFRACTION	99
2.38-2.46	0.2894	154	0.2266	2777	X-RAY DIFFRACTION	99
2.46-2.56	0.2795	133	0.2374	2824	X-RAY DIFFRACTION	100
2.56-2.67	0.267	130	0.2515	2809	X-RAY DIFFRACTION	99
2.67-2.82	0.2639	147	0.2388	2822	X-RAY DIFFRACTION	99
2.82-2.99	0.2965	164	0.2396	2783	X-RAY DIFFRACTION	99
2.99-3.22	0.2624	128	0.2332	2846	X-RAY DIFFRACTION	100
3.22-3.55	0.2938	152	0.241	2832	X-RAY DIFFRACTION	99
3.55-4.06	0.2607	167	0.209	2849	X-RAY DIFFRACTION	100
4.06-5.11	0.2626	157	0.2082	2873	X-RAY DIFFRACTION	100
5.12-48.5	0.2882	145	0.2576	3011	X-RAY DIFFRACTION	98

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	2.8457	-0.5186	0.7022	5.8944	-1.4477	3.5416	-0.0845	-0.5721	-0.0097	0.5142	0.1892	0.0275	-0.2698	-0.3806	-0.1039	0.2832	-0.0423	0.0016	0.3511	-0.0724	0.2396	-15.7753	31.1091	24.8049
2	1.7271	0.225	0.6309	0.8294	-0.4032	1.1493	-0.0488	0.0741	0.1932	-0.0526	-0.0257	0.0445	-0.0986	0.0139	0.0526	0.2155	-0.0083	0.0329	0.2047	-0.0233	0.2416	-22.9252	31.2642	1.4842
3	2.5215	0.6324	0.7278	1.1231	0.2047	2.9073	0.1658	-0.0555	-0.1515	0.0474	0.1744	-0.0152	0.311	-0.3282	-0.1504	0.2719	-0.014	0.0179	0.1666	-0.0043	0.2332	-28.3663	28.7772	-2.5618
4	1.4089	-0.1486	0.1649	1.2269	-0.7812	0.4974	0.0675	0.1048	-0.0415	0.0311	-0.0129	-0.1088	-0.0095	0.0091	-0.0719	0.3531	-0.0852	0.0152	0.2831	-0.0818	0.2597	-25.5901	26.6691	6.1645
5	1.4292	0.4699	-0.0512	0.6503	0.017	0.7265	0.1139	-0.0905	-0.0415	0.0022	-0.0319	-0.0306	-0.0446	0.025	-0.0733	0.2419	-0.0131	-0.0025	0.2124	-0.0316	0.2151	-31.1377	9.6578	11.3397
6	1.6374	1.1169	0.668	2.5721	-0.1554	1.0149	-0.0961	-0.1863	-0.3997	-0.1804	0.1085	-0.5463	0.1919	-0.0083	-0.0151	0.253	0.0103	-0.0098	0.2606	-0.0126	0.3108	-17.8153	5.4943	10.5401
7	1.4486	0.959	0.1121	1.2015	-0.02	1.0474	0.1442	-0.2191	-0.2018	0.1901	-0.1276	-0.2213	0.0648	0.0572	-0.0275	0.1824	-0.0008	-0.0294	0.2605	-0.0294	0.2135	-16.3475	15.5112	18.9602
8	2.086	-0.4608	-0.0852	4.5865	0.1085	3.1663	0.0689	0.5057	0.0642	-0.9328	-0.1605	-0.1616	-0.1884	-0.1609	0.0464	0.3272	0.0535	0.0116	0.3839	0.0403	0.2773	-59.9501	30.4425	-24.9181
9	2.07	-0.1465	-0.1937	2.1628	-0.3639	2.8137	-0.1694	0.1932	0.621	-0.0619	0.0729	-0.0496	-0.6047	-0.1958	-0.1316	0.3568	-0.0089	0.0165	0.2777	0.0169	0.3993	-50.1018	42.0826	-8.3966
10	0.5322	0.2309	0.0501	0.2534	-0.1203	0.4263	-0.0048	-0.1268	0.0527	0.0089	-0.0217	-0.0535	0.025	0.0698	0.0265	0.2516	0.0208	0.0343	0.2395	-0.0446	0.2631	-49.3572	28.2754	-2.862
11	1.4732	-0.211	0.4545	0.6643	-0.1775	1.4513	-0.0457	-0.3173	0.2245	0.1801	0.0195	0.1153	-0.1714	-0.3741	0.0333	0.2136	-0.0118	0.0616	0.2685	-0.0704	0.2711	-56.8935	28.0486	2.9682
12	2.3617	-0.8901	1.5398	1.1613	-0.8571	2.6467	0.2593	-0.234	-0.0485	-0.0598	0.027	-0.0102	0.1947	-0.0357	-0.189	0.2291	-0.0476	0.0519	0.2218	-0.0394	0.2775	-47.1853	28.7445	2.6467
13	0.9697	-0.294	0.4421	1.4241	0.4245	0.7726	-0.0451	-0.2145	0.1216	0.0238	-0.054	-0.0938	-0.0684	0.0755	0.0951	0.1364	-0.0342	0.0276	0.2676	-0.0001	0.2474	-50.006	26.7035	-6.1067
14	1.2932	-0.5256	0.0642	0.3252	-0.4013	1.2359	0.0514	-0.046	-0.0719	0.0348	-0.0047	0.086	0.0075	0.0225	-0.0449	0.2385	-0.0142	0.0019	0.2083	-0.0299	0.2103	-44.5479	9.8467	-11.1627
15	0.9804	-0.9658	0.2499	2.1298	0.2665	1.2284	-0.0285	-0.1355	-0.2585	0.1325	0.0969	0.3169	0.1285	-0.0749	-0.0776	0.2542	-0.0236	0.0213	0.2134	0.005	0.2642	-57.8303	5.5513	-10.5937
16	1.5408	-0.8829	0.1588	1.1983	-0.1293	0.9122	0.1415	0.0442	-0.0938	-0.1619	-0.0567	0.1946	-0.0144	-0.153	-0.0869	0.1926	-0.0103	-0.0015	0.2187	-0.0121	0.2154	-59.2325	15.6229	-18.9889

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 20 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21 through 107 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 108 through 129 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 130 through 155 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 156 through 229 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 230 through 265 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 266 through 321 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 3 through 19 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 20 through 41 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 42 through 70 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 71 through 107 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 108 through 129 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 130 through 155 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 156 through 229 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 230 through 265 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 266 through 321 )

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