PDB-9u3e: Monomeric sarcosine oxidase from Bacillus sp. (SoxB) Y254A mutant

ID or keywords:

Entry

Database: PDB / ID: 9u3e

Title

Monomeric sarcosine oxidase from Bacillus sp. (SoxB) Y254A 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: 1.35 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	9u3e.cif.gz	190 KB	Display	PDBx/mmCIF format
PDB format	pdb9u3e.ent.gz	142 KB	Display	PDB format
PDBx/mmJSON format	9u3e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9u3e_validation.pdf.gz	935.2 KB	Display	wwPDB validaton report
Full document	9u3e_full_validation.pdf.gz	940.5 KB	Display
Data in XML	9u3e_validation.xml.gz	41.5 KB	Display
Data in CIF	9u3e_validation.cif.gz	59.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u3/9u3e ftp://data.pdbj.org/pub/pdb/validation_reports/u3/9u3e	HTTPS FTP

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Related structure data

Related structure data	9u3bC 9u3cC 9u3dC 9u3fC 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

90 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
45 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)	72.776, 69.700, 73.665
Angle α, β, γ (deg.)	90.000, 93.749, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Monomeric sarcosine oxidase / MSOX Mass: 43982.258 Da / Num. of mol.: 2 / Mutation: Y254A 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)

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Non-polymers , 5 types, 692 molecules

#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.: 4 / 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: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.12 Å³/Da / Density % sol: 41.96 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 1.6 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: 1.35→42.41 Å / Num. obs: 150204 / % possible obs: 93.7 % / Redundancy: 4.3 % / CC_1/2: 0.996 / R_merge(I) obs: 0.082 / Net I/σ(I): 8.8
Reflection shell	Resolution: 1.35→1.37 Å / R_merge(I) obs: 0.703 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 7445 / CC_1/2: 0.619

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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: 1.35→42.408 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.963 / SU B: 0.907 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.055
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1776	7346	4.892 %
R_work	0.1554	142832	-
all	0.156	-	-
obs	-	150178	93.263 %

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: 12.088 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.003 Å²	0 Å²	-0.001 Å²
2-	-	-0.001 Å²	-0 Å²
3-	-	-	-0.002 Å²

Refinement step

Cycle: LAST / Resolution: 1.35→42.408 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5925	0	133	683	6741

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.012	6420
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5911
X-RAY DIFFRACTION	r_angle_refined_deg	1.998	1.833	8760
X-RAY DIFFRACTION	r_angle_other_deg	0.682	1.756	13723
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.26	5	825
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.999	5	30
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	5.138	20	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.943	10	1057
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.389	10	296
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	950
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	7549
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1445
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	1081
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	5443
X-RAY DIFFRACTION	r_nbtor_refined	0.183	0.2	3069
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	3220
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.133	0.2	412
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.154	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.148	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.138	0.2	24
X-RAY DIFFRACTION	r_mcbond_it	1.186	1.158	3107
X-RAY DIFFRACTION	r_mcbond_other	1.185	1.158	3107
X-RAY DIFFRACTION	r_mcangle_it	1.728	2.084	3896
X-RAY DIFFRACTION	r_mcangle_other	1.728	2.085	3897
X-RAY DIFFRACTION	r_scbond_it	2.148	1.367	3313
X-RAY DIFFRACTION	r_scbond_other	2.148	1.368	3314
X-RAY DIFFRACTION	r_scangle_it	3.191	2.41	4829
X-RAY DIFFRACTION	r_scangle_other	3.191	2.41	4830
X-RAY DIFFRACTION	r_lrange_it	3.88	13.243	7099
X-RAY DIFFRACTION	r_lrange_other	3.779	12.304	6938

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
1.35-1.385	0.274	567	0.252	10597	0.253	11895	0.953	0.961	93.8546	0.225
1.385-1.423	0.261	524	0.231	10565	0.233	11523	0.958	0.967	96.2336	0.204
1.423-1.464	0.224	494	0.206	10335	0.207	11230	0.968	0.972	96.4292	0.178
1.464-1.509	0.215	463	0.184	10039	0.185	10952	0.973	0.978	95.8912	0.157
1.509-1.559	0.202	527	0.17	9531	0.172	10564	0.975	0.981	95.2101	0.146
1.559-1.613	0.182	460	0.16	9210	0.161	10233	0.979	0.983	94.4982	0.138
1.613-1.674	0.178	414	0.158	8555	0.159	9908	0.98	0.984	90.5228	0.139
1.674-1.742	0.182	517	0.151	8566	0.153	9519	0.973	0.985	95.4197	0.137
1.742-1.82	0.176	469	0.145	8229	0.147	9138	0.979	0.986	95.1849	0.134
1.82-1.908	0.174	448	0.147	7831	0.148	8730	0.979	0.986	94.8339	0.139
1.908-2.011	0.176	370	0.152	7447	0.153	8289	0.975	0.985	94.3057	0.147
2.011-2.133	0.16	381	0.15	6967	0.15	7885	0.981	0.985	93.1896	0.147
2.133-2.28	0.159	364	0.141	6371	0.142	7410	0.984	0.987	90.8907	0.144
2.28-2.462	0.159	278	0.138	5868	0.139	6895	0.985	0.988	89.1371	0.146
2.462-2.696	0.164	288	0.14	5532	0.142	6346	0.983	0.988	91.7113	0.153
2.696-3.013	0.16	243	0.146	4950	0.147	5758	0.984	0.987	90.1876	0.164
3.013-3.476	0.172	150	0.144	4399	0.145	5117	0.982	0.987	88.8997	0.167
3.476-4.25	0.144	155	0.135	3615	0.135	4317	0.987	0.989	87.3292	0.166
4.25-5.98	0.166	138	0.149	2711	0.149	3375	0.991	0.991	84.4148	0.181
5.98-42.408	0.224	96	0.181	1514	0.183	1937	0.977	0.984	83.1182	0.218

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