PDB-4yai: Crystal structure of LigL in complex with NADH and GGE from Sphin...

ID or keywords:

Entry

Database: PDB / ID: 4yai

Title

Crystal structure of LigL in complex with NADH and GGE from Sphingobium sp. strain SYK-6

Components

C alpha-dehydrogenase

Keywords

OXIDOREDUCTASE / Short Chain Dehydrogenase/reductase SDR family

Function / homology

Function and homology information

oxidoreductase activity / nucleotide binding
Similarity search - Function

Biological species

Sphingobium sp. SYK-6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.6 Å

Authors

Pereira, J.H. / McAndrew, R.P. / Heins, R.A. / Sale, K.L. / Simmons, B.A. / Adams, P.D.

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin beta-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6.
Authors: Pereira, J.H. / Heins, R.A. / Gall, D.L. / McAndrew, R.P. / Deng, K. / Holland, K.C. / Donohue, T.J. / Noguera, D.R. / Simmons, B.A. / Sale, K.L. / Ralph, J. / Adams, P.D.

History

Deposition	Feb 17, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references
Revision 1.2	Jun 1, 2016	Group: Database references
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4yai.cif.gz	323 KB	Display	PDBx/mmCIF format
PDB format	pdb4yai.ent.gz	268.3 KB	Display	PDB format
PDBx/mmJSON format	4yai.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4yai_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	4yai_full_validation.pdf.gz	1.3 MB	Display
Data in XML	4yai_validation.xml.gz	28 KB	Display
Data in CIF	4yai_validation.cif.gz	41.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ya/4yai ftp://data.pdbj.org/pub/pdb/validation_reports/ya/4yai	HTTPS FTP

-
Related structure data

Related structure data	4y98C 4y9dC 4ya6C 4yacC 4yaeC 4yagC 4yapC 4yavC 4yan C: citing same article (ref.)
Similar structure data	1xh1-d 1xu7-3 2irw-1 3m1a-6 3rde-1 4ohc-1 3hj1-1 5il2-d 1e03-2 5c0y-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (3) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #77 - May 2006 Glucose Oxidase similarity (2) #90 - Jun 2007 Fatty Acid Synthase similarity (2)

Deposited unit

A: C alpha-dehydrogenase

B: C alpha-dehydrogenase

hetero molecules

64.3 kDa, 2 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)	125.719, 72.714, 58.874
Angle α, β, γ (deg.)	90.00, 105.17, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-610- HOH

#1: Protein	C alpha-dehydrogenase / Calpha-dehydrogenase Mass: 31332.443 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligL, SLG_33660 / Production host: Escherichia coli (E. coli) / References: UniProt: C0SUJ9
#2: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-GGE / (1S,2R)-1-(4-hydroxy-3-methoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol Mass: 320.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₂₀O₆
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.65 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Magnesium Chloride, 0.1 M Hepes pH 7.5, 25% PEG 3,350 PH range: 7.5

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97741 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97741 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 67529 / % possible obs: 100 % / Redundancy: 3.7 % / Net I/σ(I): 29.8

-
Processing

Software

Name	Version	Classification
PHENIX	1.8.4_1496	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Resolution: 1.6→50 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1611	1999	2.96 %
R_work	0.1398	-	-
obs	0.1404	67525	99.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4142	0	112	559	4813

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4334
X-RAY DIFFRACTION	f_angle_d	1.122	5882
X-RAY DIFFRACTION	f_dihedral_angle_d	12.73	1596
X-RAY DIFFRACTION	f_chiral_restr	0.041	650
X-RAY DIFFRACTION	f_plane_restr	0.005	774

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 (%)
1.6-1.6398	0.2379	144	0.2209	4686	X-RAY DIFFRACTION	99
1.6398-1.6841	0.2329	141	0.2099	4653	X-RAY DIFFRACTION	100
1.6841-1.7336	0.2253	143	0.1954	4676	X-RAY DIFFRACTION	100
1.7336-1.7896	0.2136	141	0.1789	4627	X-RAY DIFFRACTION	100
1.7896-1.8536	0.2273	142	0.1707	4664	X-RAY DIFFRACTION	100
1.8536-1.9278	0.1967	141	0.1574	4629	X-RAY DIFFRACTION	100
1.9278-2.0155	0.163	145	0.1422	4713	X-RAY DIFFRACTION	100
2.0155-2.1218	0.1481	142	0.1316	4663	X-RAY DIFFRACTION	100
2.1218-2.2547	0.1765	142	0.1324	4660	X-RAY DIFFRACTION	100
2.2547-2.4288	0.1472	143	0.1291	4693	X-RAY DIFFRACTION	100
2.4288-2.6732	0.1551	143	0.1329	4694	X-RAY DIFFRACTION	100
2.6732-3.06	0.1706	143	0.1397	4680	X-RAY DIFFRACTION	100
3.06-3.855	0.1494	144	0.1257	4713	X-RAY DIFFRACTION	100
3.855-48.2681	0.1349	145	0.1319	4775	X-RAY DIFFRACTION	100

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	4.3516	1.9851	-2.3965	3.8836	1.8006	4.6771	0.094	0.03	0.0696	-0.1667	0.0275	-0.1813	-0.159	0.2384	-0.1093	0.1159	0.0239	-0.0264	0.1748	0.0162	0.1257	53.0771	68.5337	10.1908
2	3.9844	3.1616	-2.685	5.5159	-2.0494	1.8724	-0.0191	-0.2817	-0.4509	0.0081	-0.0491	-0.3851	0.1058	0.2546	0.1018	0.171	-0.0124	-0.0484	0.2518	-0.0043	0.2098	57.724	62.092	17.2427
3	6.668	2.4376	-1.3522	2.2527	-0.4988	1.7144	0.0224	-0.0979	-0.1737	0.0793	-0.0494	-0.1909	-0.0271	0.103	0.0593	0.2081	-0.0053	-0.0559	0.2291	0.0131	0.1659	52.677	67.8418	22.435
4	1.571	1.2044	-0.0751	2.0685	-0.1472	1.1668	0.0346	-0.0702	-0.0728	0.1433	-0.0313	-0.0659	0.0382	-0.0129	-0.0031	0.1782	0.0128	-0.0224	0.1713	-0.0057	0.1532	37.8782	61.347	17.7296
5	3.2549	3.5707	1.1799	5.6941	1.0907	2.1569	0.1116	0.0426	-0.0841	0.2186	-0.0744	-0.1122	0.0706	0.0014	-0.048	0.1369	0.0313	0.0021	0.1519	-0.0053	0.1363	38.4662	64.3075	6.7844
6	2.7771	1.9847	-0.0527	3.3373	-2.4086	3.0608	0.0565	0.0616	-0.1873	-0.1186	-0.0766	-0.0666	0.139	0.0561	-0.0053	0.1141	0.0152	-0.0104	0.1201	-0.0187	0.1225	32.6167	58.2733	9.2911
7	2.882	-1.5091	-1.2539	3.2264	3.8148	4.7616	0.037	0.1369	0.2426	0.0419	-0.0314	0.0907	-0.2376	-0.0074	0.0124	0.2219	0.0301	-0.0021	0.1666	0.0291	0.1685	37.005	75.5851	8.4714
8	3.398	0.7926	-1.9128	3.6641	-2.7435	4.3737	-0.1393	-0.192	-0.7172	-0.2985	-0.1027	-0.2623	0.7779	0.382	0.2626	0.3607	0.0599	-0.0436	0.3262	-0.0222	0.4254	45.5831	47.7295	13.1278
9	4.0668	2.0595	0.637	1.75	0.1694	0.9861	-0.1072	0.4056	0.0084	-0.2327	0.1341	0.0719	0.0534	0.006	-0.0313	0.2387	0.034	-0.0101	0.2251	0.0051	0.1263	35.6946	63.1857	-2.8138
10	2.8761	1.1472	1.083	4.4172	-0.4456	1.4687	-0.0259	0.1076	0.234	-0.0546	0.1744	0.507	0.0192	-0.349	-0.1275	0.1503	-0.0004	0.0375	0.2892	0.0737	0.2903	3.6994	51.9647	12.9575
11	2.5533	0.9217	1.107	1.8079	1.6452	1.9571	0.1224	-0.253	0.5355	0.2671	-0.1259	0.7637	-0.0661	-0.5113	-0.0027	0.2645	0.0233	0.1607	0.3832	0.028	0.4896	0.506	57.0574	23.0085
12	6.5532	-0.1679	0.7984	1.1681	-0.1281	3.5263	-0.0779	-0.3255	-0.2348	0.3069	0.07	0.6446	-0.0581	-0.6261	0.1314	0.2197	0.0166	0.1162	0.2889	0.0085	0.4343	3.1304	52.7334	23.7233
13	2.2656	1.9462	2.0561	2.1282	1.3842	2.1877	0.2128	-0.5218	-0.0816	0.3504	-0.1454	0.1028	0.1582	-0.2289	-0.081	0.2694	-0.0173	0.0384	0.2929	0.0364	0.2309	12.2086	45.9485	26.8243
14	1.0164	0.5885	-0.064	1.0984	-0.3204	0.856	0.0453	-0.0687	0.0797	0.1288	-0.0057	0.1485	-0.0312	-0.0761	-0.0359	0.157	0.0172	0.0235	0.1667	-0.0109	0.1783	19.8007	57.6363	16.3479
15	1.9505	3.0902	0.5398	8.043	2.0963	1.7927	-0.0211	0.0389	0.0153	0.0159	0.0824	0.0221	0.0034	-0.0753	-0.0452	0.1397	0.0123	-0.0117	0.1702	0.0003	0.1445	23.399	56.236	9.6478
16	1.6191	0.1172	-0.0902	1.9718	1.2384	2.4972	0.0499	-0.1276	0.571	0.1812	-0.0015	0.4014	-0.3911	-0.2735	0.02	0.2719	0.0571	0.0997	0.2479	0.02	0.4213	13.0036	68.7947	17.5081
17	4.1597	2.2713	-1.0659	2.7832	-0.7927	1.0712	-0.1329	0.3893	0.2274	-0.285	0.2373	0.3177	0.0193	-0.2187	-0.1152	0.2124	0.0099	-0.057	0.2329	0.0311	0.1467	18.4465	60.7804	-1.3246

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 50 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 51 through 82 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 83 through 133 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 134 through 152 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 153 through 171 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 172 through 187 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 188 through 230 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 231 through 273 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 28 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 29 through 51 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 52 through 67 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 68 through 82 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 83 through 152 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 153 through 179 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 180 through 230 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 231 through 273 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi