PDB-5ey5: LBCATS - Yorodumi

ID or keywords:

Entry

Database: PDB / ID: 5ey5

Title

LBCATS

Components

LBCA-b
LBCATS-a

Keywords

LYASE /

complex /

Synthase

Function / homology

Rossmann fold - #1100 / Aldolase class I /

TIM Barrel / Alpha-Beta Barrel /

Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / SN-GLYCEROL-3-PHOSPHATE /

PYRIDOXAL-5'-PHOSPHATE

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.972 Å

Authors

Busch, F. / Rajendran, C. / Schlee, S. / Heyn, K. / Merkl, R. / Sterner, R.

Citation

Journal: To Be Published
Title: LBCATS
Authors: Merkl, R. / Schlee, S. / Heyn, K.

History

Deposition	Nov 24, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Apr 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ey5.cif.gz	498.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5ey5.ent.gz	410.8 KB	Display	PDB format
PDBx/mmJSON format	5ey5.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/ey/5ey5 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/5ey5	HTTPS FTP

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Related structure data

Related structure data	2j9xS S: Starting model for refinement
Similar structure data	5tcg-2 1k8x-1 5tcj-1 2clh-1 5tcf-1 5tcj-2 2rh9-1 5tch-2 1qop-1 1wbj-1 1qoq-1 1a5s-1 2trs-1 1kfc-1 2clk-1 1k3u-1 6dzo-1 1k8z-1 2clm-1 1ttq-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: LBCATS-a

B: LBCA-b

C: LBCATS-a

D: LBCA-b

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	95.963, 162.996, 78.058
Angle α, β, γ (deg.)	90.00, 93.78, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-601- HOH
2	1	B-717- HOH

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Protein , 2 types, 4 molecules ACBD

#1: Protein	LBCATS-a / Tryptophan synthase alpha chain Mass: 29958.029 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein	LBCA-b / Tryptophan synthase beta chain Mass: 43634.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 405 molecules

#3: Chemical	ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE / Glycerol 3-phosphate Mass: 172.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₉O₆P
#4: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.56 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: sodium citrate tribasic dehydrate, PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: May 14, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.972→47.25 Å / Num. obs: 81220 / % possible obs: 97 % / Observed criterion σ(I): 8.73 / Redundancy: 3.7 % / CC_1/2: 0.996 / R_merge(I) obs: 0.08159 / Net I/σ(I): 8.7
Reflection shell	Resolution: 1.972→2.043 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.4591 / Mean I/σ(I) obs: 1.93 / Num. unique all: 6804 / CC_1/2: 0.801 / % possible all: 81

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2j9x

2j9x

Resolution: 1.972→47.255 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.232	4057	5 %
R_work	0.1784	-	-
obs	0.1811	81129	96.57 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.972→47.255 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9516	0	53	398	9967

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9715
X-RAY DIFFRACTION	f_angle_d	0.851	13182
X-RAY DIFFRACTION	f_dihedral_angle_d	14.636	5845
X-RAY DIFFRACTION	f_chiral_restr	0.051	1517
X-RAY DIFFRACTION	f_plane_restr	0.006	1726

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 (%)
1.9715-1.9947	0.3852	84	0.341	1601	X-RAY DIFFRACTION	58
1.9947-2.0191	0.3545	128	0.2894	2422	X-RAY DIFFRACTION	89
2.0191-2.0446	0.3189	140	0.264	2660	X-RAY DIFFRACTION	95
2.0446-2.0715	0.2878	141	0.2311	2696	X-RAY DIFFRACTION	99
2.0715-2.0999	0.2646	144	0.216	2726	X-RAY DIFFRACTION	99
2.0999-2.1299	0.3028	143	0.2082	2727	X-RAY DIFFRACTION	99
2.1299-2.1617	0.2846	143	0.2143	2715	X-RAY DIFFRACTION	99
2.1617-2.1955	0.2617	144	0.2097	2735	X-RAY DIFFRACTION	99
2.1955-2.2315	0.2697	145	0.2051	2757	X-RAY DIFFRACTION	99
2.2315-2.2699	0.2691	141	0.218	2679	X-RAY DIFFRACTION	99
2.2699-2.3112	0.2754	145	0.2038	2739	X-RAY DIFFRACTION	99
2.3112-2.3557	0.2774	143	0.2069	2725	X-RAY DIFFRACTION	99
2.3557-2.4037	0.2497	144	0.1998	2726	X-RAY DIFFRACTION	99
2.4037-2.456	0.2524	142	0.2049	2707	X-RAY DIFFRACTION	99
2.456-2.5131	0.2541	145	0.196	2746	X-RAY DIFFRACTION	99
2.5131-2.576	0.2891	141	0.1993	2693	X-RAY DIFFRACTION	99
2.576-2.6456	0.2383	143	0.2004	2719	X-RAY DIFFRACTION	99
2.6456-2.7235	0.2639	143	0.1983	2705	X-RAY DIFFRACTION	98
2.7235-2.8114	0.2516	138	0.2019	2619	X-RAY DIFFRACTION	96
2.8114-2.9118	0.2554	135	0.2023	2566	X-RAY DIFFRACTION	93
2.9118-3.0284	0.27	142	0.1941	2696	X-RAY DIFFRACTION	98
3.0284-3.1662	0.2381	144	0.1887	2738	X-RAY DIFFRACTION	99
3.1662-3.3331	0.2748	142	0.178	2699	X-RAY DIFFRACTION	98
3.3331-3.5418	0.1843	144	0.1681	2742	X-RAY DIFFRACTION	99
3.5418-3.8152	0.181	142	0.1538	2688	X-RAY DIFFRACTION	98
3.8152-4.1989	0.1959	142	0.1438	2710	X-RAY DIFFRACTION	98
4.1989-4.806	0.1748	142	0.1308	2701	X-RAY DIFFRACTION	97
4.806-6.0531	0.2313	140	0.1647	2655	X-RAY DIFFRACTION	96
6.0531-47.2684	0.2121	147	0.1642	2780	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	3.9935	-1.9349	0.9301	8.6584	-3.0223	3.2431	-0.0989	-0.4838	-0.3922	0.4395	0.1255	0.4384	0.1072	-0.1597	-0.0553	0.2491	-0.019	0.0767	0.2598	0.0144	0.2593	-3.6851	47.3009	101.2201
2	3.8949	1.0824	0.5843	4.4373	-1.3553	3.1242	0.0865	-0.2942	-0.0805	0.4383	-0.0947	-0.0818	-0.3105	0.0334	0.0014	0.2928	0.0227	0.0014	0.2067	-0.0143	0.2285	1.293	60.1854	99.0374
3	2.9663	1.6975	-0.8672	3.0439	0.7386	7.4758	0.0495	-0.4143	-0.0981	0.5161	-0.2885	-0.3608	0.0881	0.5213	0.2496	0.4178	0.0682	-0.1676	0.3931	0.0619	0.3581	14.1809	55.1899	101.4119
4	5.3331	-0.2766	-1.7493	4.2657	-0.2373	3.0936	0.1162	0.3795	-0.1828	-0.224	-0.3935	-0.4833	0.5429	0.686	0.2331	0.411	0.1632	0.0324	0.3799	0.0596	0.4632	12.9824	45.9854	92.5575
5	6.3549	-2.0464	0.0966	2.2875	-1.242	4.3237	0.1395	0.3249	-0.2659	-0.5226	-0.0964	0.4959	0.4745	-0.0553	-0.0634	0.3891	0.0067	-0.0658	0.2606	0.0036	0.4024	-5.3969	42.2981	89.697
6	0.8633	0.5827	-0.5341	1.4529	-0.9443	1.5685	-0.0612	-0.1661	-0.2122	0.1186	-0.1337	-0.4758	-0.0153	0.2704	0.22	0.1694	-0.0058	-0.0488	0.2983	0.0062	0.3274	27.4605	75.8249	74.6345
7	7.3475	-0.2304	-3.019	3.4474	0.2029	5.6857	0.0257	0.2917	0.0678	-0.2135	0.0637	0.1702	-0.2575	-0.3301	-0.1005	0.1779	-0.0147	-0.0385	0.1835	0.0027	0.2047	11.1034	69.281	67.6948
8	3.8352	3.4489	-0.0116	5.5134	-0.7561	1.6136	0.0013	-0.1019	-0.2815	0.023	-0.0511	-0.4215	-0.0124	0.2154	0.043	0.1518	0.0282	-0.0311	0.248	0.0297	0.236	23.0477	71.9144	77.6797
9	0.9255	0.7352	-1.1679	2.6726	-2.0013	2.8541	0.2138	-0.1111	0.0836	0.4667	-0.0519	0.0564	-0.4142	0.0505	-0.1707	0.2962	-0.0278	-0.0165	0.2812	-0.0527	0.2111	16.8624	87.9861	82.1255
10	2.6263	0.9085	-1.1545	6.2628	-2.366	3.2783	-0.0972	0.6241	0.3995	-0.1722	0.2008	0.3226	-0.1802	-0.1188	-0.0753	0.3073	-0.0994	-0.061	0.4765	0.1041	0.4031	2.9907	115.47	18.7591
11	3.1016	-3.0968	-1.0302	7.269	-2.9181	4.5401	0.302	0.5027	0.2523	-0.5237	-0.491	-0.1171	0.6476	-0.0091	0.1662	0.3832	-0.1182	0.0122	0.589	0.0512	0.2506	15.18	106.3794	17.3012
12	3.7418	1.2903	2.8245	7.2994	5.6767	7.1344	-0.0751	0.7649	0.3727	-0.5271	0.276	-0.3761	-0.4868	0.7377	-0.2824	0.3248	-0.1073	0.044	0.5549	0.0912	0.364	20.6723	114.3156	18.9292
13	6.4388	-3.3501	1.275	3.0581	-2.1647	8.3339	-0.0554	0.2172	-0.0118	0.0763	0.1019	-0.4925	-0.2873	0.6101	0.0022	0.4263	-0.2222	0.004	0.5887	0.1145	0.6619	22.7651	121.0017	24.4814
14	3.9528	-2.3969	-0.0328	3.1737	-0.311	4.9246	0.0651	-0.2023	0.5068	0.4203	-0.0915	0.0128	-0.5257	-0.1998	-0.0852	0.4514	-0.0609	-0.0295	0.357	0.1241	0.6004	3.362	125.146	28.061
15	0.8524	0.0927	-0.4985	2.2746	-1.2748	1.833	-0.1734	-0.0028	-0.0484	-0.0875	0.0236	-0.2698	0.0745	0.0315	0.1497	0.1631	-0.0454	0.0083	0.2507	-0.0599	0.2718	29.5946	94.0576	48.2869
16	7.5485	2.2402	1.8188	4.4407	-0.0356	4.6625	-0.0239	-0.0978	-0.076	-0.1829	0.0715	0.1267	0.1869	-0.2827	-0.042	0.1717	0.0428	0.0205	0.2184	-0.0049	0.1799	11.9512	100.4579	51.8314
17	7.2057	-1.8751	-2.6006	3.5276	0.0434	5.3153	0.0235	0.1511	0.4469	-0.0815	0.1469	0.0072	-0.2631	-0.2917	-0.1725	0.2054	-0.0248	-0.0001	0.2302	0.0132	0.231	17.7828	106.1828	42.2133
18	5.921	-5.4092	0.754	8.0436	-1.6325	3.1536	-0.4159	-0.2505	0.0079	-0.1295	-0.0063	-0.9905	0.2455	0.3811	0.3858	0.2232	-0.0198	0.1136	0.2608	0.0053	0.4359	35.0813	88.5765	47.0257
19	1.0663	-0.7377	-1.1884	4.0549	-0.9174	2.6257	-0.5973	0.6005	-0.1723	-1.2793	0.3674	-0.4231	0.6588	-0.2573	-0.0409	0.7041	-0.139	0.1849	0.3388	-0.068	0.2678	26.9065	81.8914	37.857
20	0.4168	-1.2921	0.9314	4.656	-2.4203	3.8636	-0.025	0.199	-0.2646	-0.6913	0.2773	0.3995	0.5201	-0.8471	-0.2311	0.5277	-0.2135	-0.0003	0.4909	-0.0642	0.3123	17.8569	91.2843	31.0031
21	0.5579	0.184	0.5164	2.6325	-0.46	4.4194	-0.2725	0.2163	-0.3205	-0.8056	0.165	0.0166	0.6547	-0.443	0.1496	0.5987	-0.1965	0.0744	0.357	-0.0919	0.3252	20.1029	74.7284	45.6046

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 42 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 136 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 137 through 159 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 160 through 216 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 217 through 269 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 96 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 97 through 160 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 161 through 215 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 216 through 383 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 2 through 102 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 103 through 136 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 137 through 159 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 160 through 177 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 178 through 261 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1 through 95 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 96 through 160 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 161 through 191 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 192 through 215 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 216 through 264 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 265 through 316 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 317 through 383 )

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-Non-polymers , 4 types, 405 molecules

-Experimental details

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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Experimental details

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Yorodumi