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- PDB-9u3d: Monomeric sarcosine oxidase from Bacillus sp. (SoxB) complexed wi... -

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Basic information

Entry
Database: PDB / ID: 9u3d
TitleMonomeric sarcosine oxidase from Bacillus sp. (SoxB) complexed with D-Proline
ComponentsMonomeric sarcosine oxidase
KeywordsOXIDOREDUCTASE / Sarcosine oxidase
Function / homology
Function and homology information


sarcosine oxidase (formaldehyde-forming) / sarcosine oxidase activity / flavin adenine dinucleotide binding / cytoplasm
Similarity search - Function
Sarcosine oxidase, monomeric / MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
D-PROLINE / FLAVIN-ADENINE DINUCLEOTIDE / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. B-0618 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsZhang, Y. / Nakajima, Y. / Kurobe, M. / Nakamura, T. / Himiyama, T. / Nishiya, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K08609 Japan
CitationJournal: 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
DepositionMar 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monomeric sarcosine oxidase
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,77416
Polymers88,1492
Non-polymers2,62514
Water8,251458
1
A: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3838
Polymers44,0741
Non-polymers1,3087
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3918
Polymers44,0741
Non-polymers1,3167
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.367, 69.687, 73.095
Angle α, β, γ (deg.)90.000, 92.096, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Monomeric sarcosine oxidase / MSOX


Mass: 44074.355 Da / Num. of mol.: 2
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 , 6 types, 472 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-DPR / D-PROLINE


Type: D-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.5 M Ammonium sulfate, 100 mM Tris-HCl buffer pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.35→41.67 Å / Num. obs: 151911 / % possible obs: 97.1 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.035 / Net I/σ(I): 9
Reflection shellResolution: 1.35→1.37 Å / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7404 / CC1/2: 0.614

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EL5

1el5


Resolution: 1.35→41.67 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.998 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.055
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1828 8068 5.312 %
Rwork0.1579 143820 -
all0.159 --
obs-151888 96.833 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.318 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å20 Å20.001 Å2
2---0.002 Å2-0 Å2
3---0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.35→41.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5940 0 168 458 6566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126494
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165955
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.8398860
X-RAY DIFFRACTIONr_angle_other_deg0.6581.75713834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1625829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.167532
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg27.856202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.113101073
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.94610304
X-RAY DIFFRACTIONr_chiral_restr0.0980.2955
X-RAY DIFFRACTIONr_chiral_restr_other0.0260.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.027626
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021468
X-RAY DIFFRACTIONr_nbd_refined0.230.21054
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.25409
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23049
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2297
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.219
X-RAY DIFFRACTIONr_nbd_other0.1840.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.212
X-RAY DIFFRACTIONr_mcbond_it1.631.7393115
X-RAY DIFFRACTIONr_mcbond_other1.6181.7393115
X-RAY DIFFRACTIONr_mcangle_it2.2213.1233904
X-RAY DIFFRACTIONr_mcangle_other2.2223.1243905
X-RAY DIFFRACTIONr_scbond_it3.0172.0733379
X-RAY DIFFRACTIONr_scbond_other2.9782.0443364
X-RAY DIFFRACTIONr_scangle_it4.5623.6574918
X-RAY DIFFRACTIONr_scangle_other4.4973.6054895
X-RAY DIFFRACTIONr_lrange_it5.83719.4466973
X-RAY DIFFRACTIONr_lrange_other5.83719.4486974
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.35-1.3850.36320.289103900.29115350.9450.94995.55270.289
1.385-1.4230.2645280.264103450.264112930.9570.95896.28090.256
1.423-1.4640.2376040.2398670.23109180.9650.96795.90580.217
1.464-1.5090.2255730.20295320.203106250.970.97495.10590.186
1.509-1.5590.2185610.18693850.188103210.970.97896.36660.17
1.559-1.6130.1985010.17191340.17299420.9740.98296.91210.156
1.613-1.6740.2085030.16688680.16996760.9740.98396.84790.153
1.674-1.7420.24750.15785710.1693120.9750.98597.14350.148
1.742-1.820.194650.15581390.15788530.9780.98597.18740.148
1.82-1.9080.1844420.15278230.15484990.980.98697.24670.148
1.908-2.0110.1814300.15173890.15280980.980.98796.55470.151
2.011-2.1330.1793580.15470040.15576700.9810.98695.98440.159
2.133-2.280.1643510.14166870.14272110.9850.98897.60090.15
2.28-2.4620.1782820.14763790.14967340.9810.98798.91590.16
2.462-2.6960.1793500.1557690.15261850.9790.98698.93290.168
2.696-3.0120.1643400.15452130.15556080.9830.98599.01930.177
3.012-3.4750.172050.14747050.14849900.9820.98798.39680.174
3.475-4.2490.1531270.13439720.13442010.9840.98997.5720.167
4.249-5.9780.1562090.14529930.14532940.990.9997.2070.185
5.978-41.670.1981320.18116550.18218850.9780.98294.80110.237

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