PDB-9u3f: Monomeric sarcosine oxidase from Bacillus sp. (SoxB) Y254G mutant

ID or keywords:

Entry

Database: PDB / ID: 9u3f

Title

Monomeric sarcosine oxidase from Bacillus sp. (SoxB) Y254G mutant

Components

Monomeric sarcosine oxidase

Keywords

OXIDOREDUCTASE / Sarcosine oxidase

Function / homology

Function and homology information

sarcosine oxidase (formaldehyde-forming) / sarcosine oxidase activity / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function

Biological species

Bacillus sp. B-0618 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Zhang, Y. / Nakajima, Y. / Kurobe, M. / Nakamura, T. / Himiyama, T. / Nishiya, Y.

Funding support

Japan, 1items

Citation

Journal: Febs Open Bio / Year: 2025
Title: Structural and functional analysis of Bacillus sarcosine oxidase and its activity toward cyclic imino acids.
Authors: Zhang, Y. / Nakajima, Y. / Kurobe, M. / Nakamura, T. / Himiyama, T. / Nishiya, Y.

History

Deposition	Mar 18, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9u3f.cif.gz	184.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9u3f.ent.gz	137.4 KB	Display	PDB format
PDBx/mmJSON format	9u3f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9u3f_validation.pdf.gz	928.1 KB	Display	wwPDB validaton report
Full document	9u3f_full_validation.pdf.gz	933.9 KB	Display
Data in XML	9u3f_validation.xml.gz	40.3 KB	Display
Data in CIF	9u3f_validation.cif.gz	57.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u3/9u3f ftp://data.pdbj.org/pub/pdb/validation_reports/u3/9u3f	HTTPS FTP

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Related structure data

Related structure data	9u3bC 9u3cC 9u3dC 9u3eC 1el5S S: Starting model for refinement C: citing same article (ref.)
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

Deposited unit

A: Monomeric sarcosine oxidase

B: Monomeric sarcosine oxidase

hetero molecules

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

1

A: Monomeric sarcosine oxidase

hetero molecules

defined by author
Evidence: gel filtration
44.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Monomeric sarcosine oxidase

hetero molecules

defined by author
45 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.580, 69.673, 73.676
Angle α, β, γ (deg.)	90.000, 93.735, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Monomeric sarcosine oxidase / MSOX Mass: 43968.234 Da / Num. of mol.: 2 / Mutation: Y254G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. B-0618 (bacteria) / Gene: soxA, sox / Production host: Escherichia coli (E. coli) References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming)
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 645 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.81 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.8 M Ammonium sulfate, 100 mM Tris-HCl buffer pH8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 1.45→42.364 Å / Num. obs: 128302 / % possible obs: 99 % / Redundancy: 5.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.078 / Net I/σ(I): 11.4
Reflection shell	Resolution: 1.45→1.47 Å / R_merge(I) obs: 0.777 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6356 / CC_1/2: 0.765

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1EL5

1el5

Resolution: 1.45→42.364 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.961 / SU B: 1.191 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1857	6788	5.292 %
R_work	0.1595	121492	-
all	0.161	-	-
obs	-	128280	98.929 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 13.636 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.003 Å²	0 Å²	0.003 Å²
2-	-	0.003 Å²	0 Å²
3-	-	-	-0.001 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→42.364 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5906	0	126	645	6677

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	6186
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5629
X-RAY DIFFRACTION	r_angle_refined_deg	1.872	1.831	8395
X-RAY DIFFRACTION	r_angle_other_deg	0.654	1.748	13009
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.178	5	757
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.436	5	28
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	4.585	20	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.862	10	977
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.943	10	282
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	904
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	7225
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1393
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	1038
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	5241
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	2976
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	3038
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.137	0.2	421
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.076	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.124	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.16	0.2	35
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.139	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	1.32	1.331	3037
X-RAY DIFFRACTION	r_mcbond_other	1.319	1.331	3037
X-RAY DIFFRACTION	r_mcangle_it	1.939	2.388	3791
X-RAY DIFFRACTION	r_mcangle_other	1.943	2.39	3792
X-RAY DIFFRACTION	r_scbond_it	2.326	1.545	3149
X-RAY DIFFRACTION	r_scbond_other	2.327	1.546	3150
X-RAY DIFFRACTION	r_scangle_it	3.48	2.733	4604
X-RAY DIFFRACTION	r_scangle_other	3.48	2.733	4605
X-RAY DIFFRACTION	r_lrange_it	4.241	14.193	6803
X-RAY DIFFRACTION	r_lrange_other	4.144	13.298	6652

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.45-1.488	0.226	521	0.232	8959	0.232	9510	0.963	0.96	99.6845	0.188
1.488-1.528	0.234	452	0.21	8780	0.211	9264	0.964	0.969	99.6546	0.17
1.528-1.573	0.222	460	0.195	8520	0.197	9123	0.964	0.973	98.4325	0.157
1.573-1.621	0.201	415	0.178	8295	0.179	8787	0.972	0.978	99.1237	0.142
1.621-1.674	0.197	486	0.174	7985	0.175	8497	0.973	0.98	99.694	0.142
1.674-1.733	0.213	444	0.165	7800	0.167	8260	0.971	0.983	99.8063	0.142
1.733-1.798	0.189	430	0.157	7508	0.159	7950	0.978	0.984	99.8491	0.136
1.798-1.871	0.197	470	0.157	7180	0.159	7658	0.975	0.985	99.8955	0.139
1.871-1.954	0.169	396	0.15	6934	0.151	7353	0.982	0.986	99.6872	0.137
1.954-2.049	0.195	338	0.15	6672	0.152	7043	0.978	0.986	99.5314	0.14
2.049-2.16	0.183	301	0.151	6278	0.153	6688	0.979	0.986	98.3702	0.146
2.16-2.291	0.179	357	0.148	5930	0.15	6343	0.98	0.986	99.1171	0.143
2.291-2.448	0.17	365	0.146	5511	0.147	5952	0.982	0.987	98.7231	0.147
2.448-2.644	0.176	271	0.143	5243	0.144	5568	0.981	0.987	99.0302	0.15
2.644-2.895	0.182	210	0.153	4849	0.154	5138	0.979	0.985	98.4624	0.164
2.895-3.235	0.219	221	0.164	4297	0.166	4627	0.972	0.984	97.6443	0.182
3.235-3.732	0.163	228	0.156	3739	0.156	4109	0.984	0.987	96.5442	0.179
3.732-4.561	0.139	189	0.135	3173	0.135	3501	0.989	0.989	96.0297	0.163
4.561-6.414	0.172	167	0.161	2426	0.162	2722	0.988	0.988	95.2608	0.198
6.414-42.364	0.253	67	0.195	1413	0.197	1570	0.968	0.978	94.2675	0.244

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