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- PDB-7exs: Thermomicrobium roseum sarcosine oxidase mutant - S320R -

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Basic information

Entry
Database: PDB / ID: 7exs
TitleThermomicrobium roseum sarcosine oxidase mutant - S320R
ComponentsSarcosine oxidase
KeywordsOXIDOREDUCTASE / N-demethylase / Extremely stable / Chiral specificity
Function / homologysarcosine oxidase (formaldehyde-forming) / sarcosine oxidase activity / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Sarcosine oxidase
Function and homology information
Biological speciesThermomicrobium roseum DSM 5159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsXin, Y. / Shen, C. / Tang, M.W. / Shi, Y. / Guo, Z.T. / Gu, Z.H. / Shao, J. / Zhang, L.
Citation
Journal: J.Biol.Chem. / Year: 2022
Title: Recreating the natural evolutionary trend in key microdomains provides an effective strategy for engineering of a thermomicrobial N-demethylase.
Authors: Xin, Y. / Shen, C. / Tang, M. / Guo, Z. / Shi, Y. / Gu, Z. / Shao, J. / Zhang, L.
#1: Journal: International Journal of Biological Macromolecules / Year: 2021
Title: Promote the expression and corrected folding of an extremely stable N-demethylase by promoter reconstruction, native environment simulation and surface design
Authors: Gao, Q.Y. / Shao, J. / Tang, M.W. / Xin, Y. / Zhang, L.
History
DepositionMay 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 23, 2022Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,24718
Polymers41,3761
Non-polymers1,87117
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-8 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.362, 47.141, 64.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sarcosine oxidase


Mass: 41376.301 Da / Num. of mol.: 1 / Mutation: S320R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomicrobium roseum DSM 5159 (bacteria)
Strain: DSM 5159 / Gene: trd_1773 / Production host: Bacillus subtilis (bacteria)
References: UniProt: B9L163, sarcosine oxidase (formaldehyde-forming)

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Non-polymers , 5 types, 282 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / 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.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Bis, tris, ammonium sulfate

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Data collection

DiffractionMean temperature: 291.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Jan 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.42→65.18 Å / Num. obs: 76088 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 14.4
Reflection shellResolution: 1.42→1.5 Å / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 10967

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GF3

2gf3


Resolution: 1.42→65.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.297 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 3705 4.9 %RANDOM
Rwork0.1904 ---
obs0.1917 72149 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.35 Å2 / Biso mean: 21.013 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2---1.06 Å20 Å2
3----1.09 Å2
Refinement stepCycle: final / Resolution: 1.42→65.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 111 265 3292
Biso mean--25.81 29.94 -
Num. residues----372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223127
X-RAY DIFFRACTIONr_angle_refined_deg2.3771.9924253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83821.448145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19815480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3361539
X-RAY DIFFRACTIONr_chiral_restr0.1620.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.0212397
LS refinement shellResolution: 1.421→1.458 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 260 -
Rwork0.286 5292 -
all-5552 -
obs--99.89 %

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