PDB-4ysh: Crystal structure of glycine oxidase from Geobacillus kaustophilus

ID or keywords:

Entry

Database: PDB / ID: 4ysh

Title

Crystal structure of glycine oxidase from Geobacillus kaustophilus

Components

Glycine oxidase

Keywords

OXIDOREDUCTASE / flavoprotein / glycine oxidase / substrate inhibition

Function / homology

Function and homology information

glycine oxidase / glycine oxidase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / amino acid metabolic process / FAD binding / protein homotetramerization / cytoplasm
Similarity search - Function

Biological species

Geobacillus kaustophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.2 Å

Authors

Shiono, T. / Nomura, T. / Arai, R.

Funding support

Japan, 1items

Citation

Journal: to be published
Title: Crystal structure of glycine oxidase from Geobacillus kaustophilus
Authors: Shiono, T. / Arai, R. / Nishiya, Y. / Nomura, T.

History

Deposition	Mar 17, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 5, 2020	Group: Data collection / Derived calculations Category: diffrn_source / pdbx_struct_oper_list / pdbx_struct_special_symmetry Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ysh.cif.gz	300.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4ysh.ent.gz	243.9 KB	Display	PDB format
PDBx/mmJSON format	4ysh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ysh_validation.pdf.gz	958.1 KB	Display	wwPDB validaton report
Full document	4ysh_full_validation.pdf.gz	975.1 KB	Display
Data in XML	4ysh_validation.xml.gz	31.1 KB	Display
Data in CIF	4ysh_validation.cif.gz	42.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ys/4ysh ftp://data.pdbj.org/pub/pdb/validation_reports/ys/4ysh	HTTPS FTP

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Related structure data

Related structure data	1ryiS S: Starting model for refinement
Similar structure data	1ryi-1 3if9-1 1ng3-1 6pxs-d 4dib-2 4dib-1 3if9-2 1ng4-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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	#235 - Jul 2019 AMPA Receptor similarity (1) #70 - Oct 2005 Designer Proteins similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: Glycine oxidase

B: Glycine oxidase

hetero molecules

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

1

A: Glycine oxidase

B: Glycine oxidase

hetero molecules

A: Glycine oxidase

B: Glycine oxidase

hetero molecules

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

Unit cell

Length a, b, c (Å)	87.945, 87.945, 413.456
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

Symmetry

Point symmetry: (Schoenflies symbol: C₂ (2 fold cyclic))

Components on special symmetry positions

ID	Model	Components
1	1	B-406- SO4

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Protein , 1 types, 2 molecules AB

#1: Protein	Glycine oxidase Mass: 39884.465 Da / Num. of mol.: 2 / Mutation: A139del Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria) Strain: HTA426 / Gene: GK0623 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5L2C2, glycine oxidase

#1: Protein

Glycine oxidase

Mass: 39884.465 Da / Num. of mol.: 2 / Mutation: A139del
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Geobacillus kaustophilus (strain HTA426) (bacteria)
Strain: HTA426 / Gene: GK0623 / Plasmid: pET3a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q5L2C2, glycine oxidase

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Non-polymers , 6 types, 193 molecules

#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.89 Å³/Da / Density % sol: 57.41 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 0.1 M phosphate-citrate buffer, 7% 2-propanol, 0.4 M LiSO4

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Data collection

Diffraction

Mean temperature: 95 K

Diffraction source

Source:

SYNCHROTRON / Site:

Photon Factory

/ Beamline: AR-NE3A / Wavelength: 1 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 1, 2014

Radiation

Monochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.2→50 Å / Num. obs: 48899 / % possible obs: 98.6 % / Redundancy: 20.6 % / B_iso Wilson estimate: 34.4 Å² / R_merge(I) obs: 0.096 / R_pim(I) all: 0.022 / R_rim(I) all: 0.098 / Χ²: 1 / Net I/av σ(I): 32.785 / Net I/σ(I): 11.5 / Num. measured all: 1006443

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.2-2.28	22.2	0.417	10.5	4774	0.972	0.089	0.426	0.958	99.7
2.28-2.37	22.1	0.352		4832	0.982	0.075	0.36	1.002	99.8
2.37-2.48	22	0.265		4814	0.988	0.057	0.272	1.032	99.8
2.48-2.61	21.9	0.229		4867	0.99	0.049	0.235	1.026	99.8
2.61-2.77	21.6	0.169		4880	0.994	0.036	0.173	1.037	99.9
2.77-2.99	21.4	0.124		4894	0.996	0.027	0.128	0.983	99.9
2.99-3.29	20.9	0.097		4924	0.997	0.022	0.1	1.029	99.9
3.29-3.76	19.9	0.075		4985	0.998	0.017	0.077	0.965	100
3.76-4.74	18	0.066		4997	0.997	0.016	0.068	0.967	98.3
4.74-50	15.9	0.064		4932	0.997	0.016	0.066	0.993	90.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling
MOLREP	10.2.35	phasing
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB 1RYI

1ryi

Resolution: 2.2→50 Å / Cor.coef. F_o:F_c: 0.915 / Cor.coef. F_o:F_c free: 0.897 / WR_factor R_free: 0.2682 / WR_factor R_work: 0.2314 / FOM work R set: 0.8341 / SU B: 13.612 / SU ML: 0.163 / SU R Cruickshank DPI: 0.2666 / SU R_free: 0.2137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2661	2463	5.1 %	RANDOM
R_work	0.2328	-	-	-
obs	0.2345	46153	98.34 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 139.76 Å² / B_iso mean: 44.542 Å² / B_iso min: 24.03 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.66 Å²	0.33 Å²	0 Å²
2-	-	0.66 Å²	0 Å²
3-	-	-	-0.99 Å²

Refinement step

Cycle: final / Resolution: 2.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5510	0	136	184	5830
B_iso mean	-	-	42.88	45.06	-
Num. residues	-	-	-	-	738

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	5807
X-RAY DIFFRACTION	r_angle_refined_deg	1.344	1.995	7915
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.804	5	746
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.05	22.356	225
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.227	15	889
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.13	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	891
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	4390
X-RAY DIFFRACTION	r_mcbond_it	0.429	1.5	3666
X-RAY DIFFRACTION	r_mcangle_it	0.804	2	5826
X-RAY DIFFRACTION	r_scbond_it	1.099	3	2141
X-RAY DIFFRACTION	r_scangle_it	1.885	4.5	2084

LS refinement shell

Resolution: 2.201→2.258 Å

	R_factor	Num. reflection	% reflection
R_free	0.307	182	5.2 %
R_work	0.271	3321	-
obs	-	-	98.95 %

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	4.7282	0.7273	-0.2901	2.0913	0.5704	1.2581	0.0137	-0.714	-0.3964	0.266	-0.1256	0.2142	0.1327	-0.1644	0.1118	0.2453	0.0501	0.0349	0.4755	0.0585	0.2991	-72.3406	12.7226	13.149
2	9.0896	-1.8888	3.2612	4.0098	-2.3582	2.8663	-0.1152	-0.2922	1.6267	-0.1189	-0.1826	0.0152	-0.1092	-0.1537	0.2977	0.1575	0.1103	0.007	0.317	-0.1359	0.4737	-66.5174	28.3152	9.3723
3	0.966	-0.7299	1.2047	4.4638	-5.0526	7.95	0.0151	-0.0805	0.1535	-0.1771	-0.0213	0.0718	-0.341	-0.327	0.0062	0.3611	0.0976	-0.0283	0.2795	-0.0026	0.3346	-57.8757	30.5968	-2.6937
4	12.2496	-6.6978	-3.0256	10.2916	3.5289	5.7202	-0.3403	-0.2828	0.667	-0.6217	-0.0992	-0.2187	-0.8752	-0.5636	0.4396	0.4591	0.1361	-0.0778	0.1187	-0.0357	0.2171	-59.0392	41.5522	-4.5562
5	1.7517	-0.2618	0.0957	0.8367	-0.2759	1.8846	-0.0453	0.0067	0.1757	-0.3725	0.1014	-0.0854	-0.1467	-0.1688	-0.0561	0.3983	0.0574	0.0173	0.3211	-0.024	0.3831	-56.3776	25.9044	1.4097
6	7.7851	7.3807	0.1585	9.3625	0.7767	2.0647	-0.3966	-1.2481	-2.5986	0.1128	-0.0998	0.2371	0.0859	-0.31	0.4963	0.0165	0.1713	0.3388	0.405	0.6161	1.7255	-80.4191	2.7922	12.0183
7	2.8716	0.504	-0.7343	1.2234	-0.2293	1.1209	-0.1104	0.1626	-0.0082	-0.0652	0.0338	0.1764	-0.0538	-0.2536	0.0766	0.3005	0.0718	0.0056	0.3968	-0.0193	0.2844	-68.8031	16.4844	-1.2493
8	2.1767	0.7026	0.1305	1.544	1.0588	0.987	0.0547	0.196	-0.0845	-0.1457	-0.0362	0.0063	-0.0984	-0.2966	-0.0186	0.3218	0.0706	0.0287	0.3674	0.0213	0.2986	-56.9699	17.2739	-9.8248
9	10.5537	2.2736	-1.3041	1.7398	-0.5971	2.0166	0.1755	-0.0509	-0.0839	-0.1254	-0.1735	-0.095	-0.1342	-0.042	-0.002	0.323	0.0487	0.0124	0.3244	-0.033	0.2824	-52.4605	14.7361	-7.7554
10	9.8367	2.1869	-5.4167	4.1606	-2.0041	7.1218	-0.0657	0.5032	0.2844	-0.0603	0.2497	0.3756	0.06	-0.8297	-0.184	0.1465	0.0916	0.0161	0.5074	0.0116	0.3115	-84.146	19.0611	4.2397
11	6.5456	0.2819	-0.9931	1.7706	-1.1215	2.9169	0.0157	-0.0538	0.7609	0.0159	-0.1193	0.1734	-0.314	-0.4941	0.1036	0.1787	0.1258	0.0014	0.4042	-0.1168	0.3981	-78.9988	24.7425	8.1977
12	2.717	-0.1376	0.4996	4.7584	1.2431	3.1743	0.0652	0.3523	0.1336	-0.514	0.0577	-0.2923	-0.3375	0.3569	-0.1228	0.3562	-0.0488	0.0231	0.3651	-0.0051	0.2751	-26.689	18.5563	7.6845
13	0.8068	1.2274	1.329	11.453	4.0496	4.2458	-0.3168	0.2654	0.3663	-0.8912	-0.0999	0.3029	-0.8344	0.0292	0.4167	0.3634	-0.0645	0.0127	0.4119	0.0387	0.3244	-26.1756	23.9057	7.4493
14	0.925	0.2345	-0.2864	0.1539	0.1378	1.3966	0.0609	0.0187	-0.1089	-0.0141	0.0618	-0.0783	0.0327	-0.0145	-0.1227	0.342	-0.0331	-0.0015	0.33	-0.0129	0.334	-33.5026	7.9405	21.9203
15	1.5991	0.0807	-0.0692	1.1063	-0.6378	2.0695	0.0257	-0.014	0.1918	0.0533	-0.0062	0.0287	-0.2657	-0.1894	-0.0195	0.3485	-0.0042	-0.0015	0.3391	-0.0187	0.2926	-43.6131	17.4818	21.2768
16	4.2776	1.2263	1.2957	1.1653	0.7303	2.278	0.1101	-0.2955	-0.1895	0.1729	-0.1109	0.066	0.2135	-0.3916	0.0008	0.3388	-0.0744	0.002	0.3894	0.0139	0.2432	-44.3061	1.6682	40.6996
17	1.3058	-0.1378	-0.2158	0.8092	0.1584	2.0394	-0.0039	0.1233	-0.0454	-0.1151	0.0101	-0.0772	0.0527	0.0097	-0.0063	0.3541	-0.0204	-0.0217	0.3439	-0.0293	0.3433	-34.4548	10.2875	13.6738
18	1.2276	0.2257	0.1743	0.8585	-0.1632	4.1488	-0.006	0.2703	-0.0743	-0.3396	0.0477	-0.2544	-0.0562	0.3041	-0.0417	0.3195	-0.0267	0.0719	0.3968	-0.0733	0.3197	-20.8368	9.4604	3.971
19	2.4476	0.388	-0.7759	0.6258	0.1578	1.3515	-0.0311	-0.101	-0.1313	0.0559	0.0252	-0.0698	0.1682	-0.0238	0.0059	0.3098	-0.022	-0.0314	0.3425	-0.0069	0.32	-38.3077	-0.3183	19.4434
20	3.1772	0.0681	-0.5441	1.0022	0.2596	0.866	-0.0196	0.0233	-0.3026	-0.0482	0.0078	-0.1013	0.1464	-0.0731	0.0118	0.3157	-0.0453	-0.0176	0.322	-0.0098	0.3148	-44.2686	-5.2646	17.5239
21	3.5472	0.8899	-0.2706	1.3275	0.6293	1.9727	0.0778	-0.1231	-0.1241	0.1212	-0.0654	0.0573	0.0732	-0.3662	-0.0124	0.3048	-0.0524	0.0023	0.3127	-0.0065	0.2939	-51.758	-5.8334	19.726
22	3.5629	1.6133	-0.7882	4.6029	-1.1151	3.6776	0.0177	-0.0081	-0.2485	0.0027	0.0017	-0.3227	0.072	0.2568	-0.0194	0.3039	0.0144	-0.0163	0.3761	-0.0644	0.3049	-20.1465	6.8379	17.9403
23	2.4906	0.2514	-0.3822	1.0099	-0.2735	3.0657	-0.0127	-0.0137	-0.1052	-0.004	0.0511	-0.1748	-0.0762	0.2181	-0.0385	0.3308	-0.0082	-0.0011	0.3446	-0.0388	0.3173	-23.2239	13.5809	22.4263

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 53
2	X-RAY DIFFRACTION	2	A	54 - 83
3	X-RAY DIFFRACTION	3	A	84 - 107
4	X-RAY DIFFRACTION	4	A	108 - 134
5	X-RAY DIFFRACTION	5	A	135 - 166
6	X-RAY DIFFRACTION	6	A	167 - 197
7	X-RAY DIFFRACTION	7	A	198 - 251
8	X-RAY DIFFRACTION	8	A	252 - 293
9	X-RAY DIFFRACTION	9	A	294 - 308
10	X-RAY DIFFRACTION	10	A	309 - 332
11	X-RAY DIFFRACTION	11	A	333 - 371
12	X-RAY DIFFRACTION	12	B	2 - 25
13	X-RAY DIFFRACTION	13	B	26 - 32
14	X-RAY DIFFRACTION	14	B	33 - 69
15	X-RAY DIFFRACTION	15	B	70 - 97
16	X-RAY DIFFRACTION	16	B	98 - 136
17	X-RAY DIFFRACTION	17	B	137 - 189
18	X-RAY DIFFRACTION	18	B	190 - 213
19	X-RAY DIFFRACTION	19	B	214 - 249
20	X-RAY DIFFRACTION	20	B	250 - 286
21	X-RAY DIFFRACTION	21	B	287 - 307
22	X-RAY DIFFRACTION	22	B	308 - 334
23	X-RAY DIFFRACTION	23	B	335 - 369

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Protein , 1 types, 2 molecules AB

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-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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 6 types, 193 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
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

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Yorodumi