PDB-8zka: Crystal structure of the Decarboxylase KDC4427 in complex with ph...

ID or keywords:

Entry

Database: PDB / ID: 8zka

Title

Crystal structure of the Decarboxylase KDC4427 in complex with phenylpyruvic acid intermediate

Components

Indolepyruvate decarboxylase

Keywords

LYASE / Decarboxylase

Function / homology

Function and homology information

indolepyruvate decarboxylase activity / auxin biosynthetic process / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / cytosol
Similarity search - Function

Biological species

Enterobacter sp. CGMCC 5087 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Dong, S. / Liu, L. / Zhang, H.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the Decarboxylase KDC4427 in complex with phenylpyruvic acid intermediate
Authors: Dong, S. / Liu, L. / Zhang, H.

History

Deposition	May 15, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 21, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8zka.cif.gz	444.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8zka.ent.gz		Display	PDB format
PDBx/mmJSON format	8zka.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/zk/8zka ftp://data.pdbj.org/pub/pdb/validation_reports/zk/8zka	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (10) #213 - Sep 2017 Sirtuins similarity (1) #153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1)

Deposited unit

A: Indolepyruvate decarboxylase

B: Indolepyruvate decarboxylase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	138.410, 170.120, 115.600
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-703- HOH
2	1	A-738- HOH
3	1	B-1050- HOH

#1: Protein	Indolepyruvate decarboxylase / KDC4427 Mass: 61957.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter sp. CGMCC 5087 (bacteria) / Gene: ipdC, DEO48_12930 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U3EYQ2
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-A1L14 / 2-[(2~{E})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2-(1-oxidanyl-2-phenyl-ethylidene)-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate Mass: 544.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₆N₄O₈P₂S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1021 / 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: 2.75 Å³/Da / Density % sol: 55.2 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M calcium acetate, 0.1M sodium MES, pH 6.0, 13% PEG 400

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 30, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.95→107.36 Å / Num. obs: 98138 / % possible obs: 99 % / Redundancy: 6.5 % / CC_1/2: 0.992 / R_merge(I) obs: 0.206 / R_pim(I) all: 0.087 / R_rim(I) all: 0.224 / Χ²: 1 / Net I/σ(I): 8.3 / Num. measured all: 642742
Reflection shell	Resolution: 1.95→2 Å / % possible obs: 99.6 % / Redundancy: 6.9 % / R_merge(I) obs: 1.435 / Num. measured all: 49890 / Num. unique obs: 7237 / CC_1/2: 0.598 / R_pim(I) all: 0.58 / R_rim(I) all: 1.549 / Χ²: 0.88 / Net I/σ(I) obs: 1.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
Aimless		data scaling
xia2		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→85.06 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.96 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2301	3823	2.04 %
R_work	0.2073	-	-
obs	0.2077	87311	97.43 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→85.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8210	0	72	1021	9303

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	8475
X-RAY DIFFRACTION	f_angle_d	0.869	11559
X-RAY DIFFRACTION	f_dihedral_angle_d	7.585	1162
X-RAY DIFFRACTION	f_chiral_restr	0.108	1310
X-RAY DIFFRACTION	f_plane_restr	0.007	1497

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 (%)
1.95-1.97	0.3578	141	0.338	6837	X-RAY DIFFRACTION	98
1.97-2	0.3501	145	0.3222	6866	X-RAY DIFFRACTION	98
2-2.03	0.2928	146	0.3131	6910	X-RAY DIFFRACTION	98
2.03-2.06	0.5102	122	0.5152	5800	X-RAY DIFFRACTION	84
2.06-2.09	0.341	141	0.2935	6882	X-RAY DIFFRACTION	98
2.09-2.12	0.3055	146	0.2635	6928	X-RAY DIFFRACTION	99
2.12-2.16	0.2555	141	0.2562	6902	X-RAY DIFFRACTION	99
2.16-2.19	0.2309	147	0.2471	6863	X-RAY DIFFRACTION	99
2.19-2.23	0.3756	103	0.3108	5060	X-RAY DIFFRACTION	73
2.23-2.28	0.2928	145	0.2422	6856	X-RAY DIFFRACTION	98
2.28-2.32	0.2454	141	0.2182	6877	X-RAY DIFFRACTION	99
2.32-2.37	0.2293	144	0.2171	6963	X-RAY DIFFRACTION	99
2.37-2.43	0.2505	139	0.2104	6905	X-RAY DIFFRACTION	99
2.43-2.49	0.2872	141	0.2079	6948	X-RAY DIFFRACTION	99
2.49-2.56	0.2429	148	0.2065	6901	X-RAY DIFFRACTION	99
2.56-2.63	0.2306	146	0.2136	6893	X-RAY DIFFRACTION	99
2.63-2.72	0.2578	142	0.247	6848	X-RAY DIFFRACTION	98
2.72-2.81	0.2384	146	0.2031	6988	X-RAY DIFFRACTION	99
2.81-2.92	0.2104	144	0.1881	6868	X-RAY DIFFRACTION	100
2.92-3.06	0.2281	146	0.1807	7020	X-RAY DIFFRACTION	100
3.06-3.22	0.1975	141	0.1714	6963	X-RAY DIFFRACTION	100
3.22-3.42	0.1912	145	0.1772	6815	X-RAY DIFFRACTION	98
3.42-3.69	0.1968	140	0.1649	6913	X-RAY DIFFRACTION	99
3.69-4.06	0.1823	140	0.1604	6866	X-RAY DIFFRACTION	98
4.06-4.64	0.1779	149	0.1369	6910	X-RAY DIFFRACTION	100
4.64-5.85	0.1613	146	0.1597	6960	X-RAY DIFFRACTION	100
5.85-85.06	0.1718	148	0.1782	6946	X-RAY DIFFRACTION	99

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	0.9613	0.3736	-0.0505	0.9726	-0.0344	0.7254	0.0104	0.0624	-0.0451	-0.0617	-0.0393	-0.0606	0.0775	0.0157	0.028	0.1086	0.0146	0.0026	0.1594	-0.0023	0.1286	19.8216	45.8297	-27.5115
2	1.4298	-0.2999	0.2568	1.6588	0.2805	0.2194	0.0368	0.2578	0.0316	-0.3216	-0.0906	-0.0879	-0.0116	0.0773	0.1054	0.1859	0.0121	0.0453	0.1701	-0.0074	0.1215	19.8446	47.9888	-40.4845
3	0.7253	-0.0061	0.4027	1.0343	-0.5746	2.1179	-0.0832	0.0964	0.1539	0.0616	-0.038	-0.1337	-0.212	0.1614	0.1006	0.1649	-0.0347	-0.017	0.1653	0.0692	0.2078	25.0386	79.9881	-38.9912
4	0.8317	-0.0727	1.7962	0.8333	-0.73	5.4551	-0.2446	0.2608	0.379	0.0573	-0.1758	-0.2674	-0.687	0.5689	0.2301	0.2045	-0.0082	-0.046	0.3103	0.0975	0.3796	34.3516	80.5029	-33.9016
5	0.9543	0.2451	0.4539	1.0885	-0.07	1.1628	-0.0263	-0.0815	0.1285	0.0963	-0.0567	-0.1091	-0.1473	0.0426	0.0702	0.1201	-0.0179	-0.0382	0.1723	0.0337	0.1982	31.6591	66.2392	-14.9361
6	1.5444	1.3818	-0.4936	1.3308	0.023	2.4868	0.0109	0.0698	0.3155	0.0244	-0.1483	0.068	-0.4257	-0.0722	0.0788	0.2045	0.002	-0.0915	0.2743	0.0409	0.2982	38.3219	69.1668	-9.5316
7	0.8717	0.0691	0.0119	0.6269	-0.0121	0.6413	-0.0237	-0.102	0.1175	0.1121	0.0109	0.0375	-0.0883	-0.1234	0.0354	0.1474	0.0348	-0.0072	0.1797	-0.0075	0.1332	5.9049	63.0196	-9.9596
8	0.6219	0.1371	0.2313	0.5283	0.3081	0.5784	0.038	-0.1963	0.098	0.0905	-0.1224	0.1916	-0.037	-0.1898	-0.0011	0.1871	0.0262	0.0244	0.251	-0.0366	0.2097	-6.6697	60.7824	-6.9469
9	1.1558	-0.0184	0.0769	0.6746	-0.271	0.6627	0.0478	-0.2062	-0.2384	0.0584	0.0199	0.002	0.1207	-0.0578	-0.0259	0.1866	-0.0507	0.0128	0.2313	0.0534	0.1819	-3.9249	28.8324	-2.3401
10	2.2999	0.8999	-0.2053	0.344	-0.0804	0.0153	-0.0581	-0.6404	-0.5436	0.1664	0.058	-0.1919	0.0024	0.0435	-0.0506	0.2194	0.0036	0.0093	0.4021	0.0734	0.2751	-2.1506	27.137	6.2889
11	1.6549	0.1612	0.2815	0.8328	-0.1967	0.3701	0.0118	-0.1233	-0.1633	0.2114	-0.0056	-0.0945	0.0248	-0.0068	0.0473	0.1761	-0.0062	-0.0302	0.1785	0.024	0.1122	17.3874	41.9599	2.2082
12	2.3916	0.3737	0.1146	0.8753	-0.4224	1.0672	0.0042	0.4758	-0.4533	-0.2153	-0.0975	-0.2137	0.2843	0.0533	0.0887	0.2836	0.013	-0.0497	0.3487	0.03	0.2943	27.2097	39.5125	-7.4491
13	1.9658	-0.4926	-0.1899	2.9775	-1.8409	1.296	0.0031	-0.0631	-0.1088	0.4071	0.0136	-0.1569	-0.0083	0.1812	0.1126	0.2101	-0.0066	-0.0948	0.19	0.0391	0.2365	33.1384	48.4558	2.5957
14	2.1256	-0.8433	-0.9226	2.6791	-1.1905	1.9819	-0.0158	0.2426	-0.6018	-0.0022	-0.1985	-0.0937	0.4938	-0.3527	0.1258	0.3052	-0.0249	-0.0393	0.396	-0.0057	0.3278	25.415	35.3438	2.617

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 144 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 145 through 191 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 192 through 323 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 324 through 370 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 371 through 488 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 489 through 548 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 3 through 144 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 145 through 191 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 192 through 323 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 324 through 361 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 362 through 450 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 451 through 479 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 480 through 506 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 507 through 548 )

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