[English] 日本語
Yorodumi
- PDB-9u3b: Monomeric sarcosine oxidase from Bacillus sp. (SoxB) complexed wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9u3b
TitleMonomeric sarcosine oxidase from Bacillus sp. (SoxB) complexed with L-Thioproline
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
FLAVIN-ADENINE DINUCLEOTIDE / THIOPROLINE / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. B-0618 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,78815
Polymers88,1492
Non-polymers2,63913
Water11,205622
1
A: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4388
Polymers44,0741
Non-polymers1,3647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3507
Polymers44,0741
Non-polymers1,2756
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.876, 69.401, 73.028
Angle α, β, γ (deg.)90.000, 93.722, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
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)

-
Non-polymers , 6 types, 635 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-PRS / THIOPROLINE


Type: L-peptide linking / Mass: 133.169 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO2S / 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.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.5 M Ammonium sulfate, 100 mM Tris-HCl buffer pH8.5

-
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: 1.3→42.24 Å / Num. obs: 165675 / % possible obs: 93.2 % / Redundancy: 2.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.8
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7948 / CC1/2: 0.651

-
Processing

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

1el5


Resolution: 1.3→40.505 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.872 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1753 8108 4.894 %
Rwork0.1529 157563 -
all0.154 --
obs-165671 92.977 %
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: 14.385 Å2
Baniso -1Baniso -2Baniso -3
1--0.006 Å2-0 Å2-0 Å2
2--0.001 Å20 Å2
3---0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.3→40.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5991 0 169 622 6782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0126551
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165997
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.8398940
X-RAY DIFFRACTIONr_angle_other_deg0.651.75513946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1895837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.827529
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg6.912202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.511101071
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.45210305
X-RAY DIFFRACTIONr_chiral_restr0.0970.2967
X-RAY DIFFRACTIONr_chiral_restr_other0.0640.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.027673
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021453
X-RAY DIFFRACTIONr_nbd_refined0.2270.21056
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.25497
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23108
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.23223
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2383
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0920.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2970.215
X-RAY DIFFRACTIONr_nbd_other0.2570.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.219
X-RAY DIFFRACTIONr_mcbond_it1.3441.3653154
X-RAY DIFFRACTIONr_mcbond_other1.3441.3653154
X-RAY DIFFRACTIONr_mcangle_it1.9962.4533950
X-RAY DIFFRACTIONr_mcangle_other1.9962.4533951
X-RAY DIFFRACTIONr_scbond_it2.5271.6253397
X-RAY DIFFRACTIONr_scbond_other2.5261.6253397
X-RAY DIFFRACTIONr_scangle_it3.8382.8644952
X-RAY DIFFRACTIONr_scangle_other3.8382.8654953
X-RAY DIFFRACTIONr_lrange_it4.70915.3247113
X-RAY DIFFRACTIONr_lrange_other4.70915.3267114
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
1.3-1.3340.2985290.288113110.288131790.9410.94289.83990.265
1.334-1.370.2755490.262107010.263127360.9460.95188.33230.237
1.37-1.410.2545910.248106950.248124530.9560.95790.62880.217
1.41-1.4530.2266170.216105070.217120850.9650.96892.0480.189
1.453-1.5010.2055950.18102600.182117100.9720.97892.69850.159
1.501-1.5530.2055670.1799330.172113630.9720.98192.40520.153
1.553-1.6120.1824950.15395980.155109180.9790.98592.44370.14
1.612-1.6780.1684780.14792520.148105000.9820.98692.66670.139
1.678-1.7520.1644500.1489000.142100940.9830.98892.62930.139
1.752-1.8380.1744600.14184880.14397220.9810.98892.03870.142
1.838-1.9370.1654450.13880980.13992020.9830.98892.83850.143
1.937-2.0540.173740.13978620.14186890.9840.98994.78650.148
2.054-2.1950.173520.13975020.1481840.9830.98995.96770.152
2.195-2.3710.1643270.13470360.13576430.9840.9996.33650.15
2.371-2.5960.1523650.13264270.13370360.9860.98996.53210.154
2.596-2.9010.1542650.13858880.13963680.9850.98896.62370.166
2.901-3.3470.1572290.14651780.14756530.9840.98795.64830.179
3.347-4.0920.151780.13344650.13447730.9870.98997.27630.168
4.092-5.7580.1591680.1434780.14137240.9880.99197.90550.182
5.758-40.5050.203740.17819840.17921460.9760.98395.89940.232

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more