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- PDB-3m13: Crystal Structure of the Lys265Arg PEG-crystallized mutant of mon... -

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Basic information

Entry
Database: PDB / ID: 3m13
TitleCrystal Structure of the Lys265Arg PEG-crystallized mutant of monomeric sarcosine oxidase
ComponentsMonomeric sarcosine oxidase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN OXIDASE / FAD / Flavoprotein
Function / homology
Function and homology information


sarcosine oxidase (formaldehyde-forming) / L-lysine catabolic process to acetyl-CoA via L-pipecolate / L-pipecolate oxidase activity / saccharopine oxidase activity / sarcosine oxidase activity / peroxisome / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
Sarcosine oxidase, monomeric / MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...Sarcosine oxidase, monomeric / MTOX family / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMathews, F.S. / Chen, Z.-W. / Jorns, M.S.
CitationJournal: Biochemistry / Year: 2010
Title: Structural characterization of mutations at the oxygen activation site in monomeric sarcosine oxidase.
Authors: Jorns, M.S. / Chen, Z.W. / Mathews, F.S.
History
DepositionMar 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)175,99114
Polymers172,5174
Non-polymers3,47410
Water8,953497
1
A: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9503
Polymers43,1291
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0454
Polymers43,1291
Non-polymers9163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9503
Polymers43,1291
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0454
Polymers43,1291
Non-polymers9163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.296, 69.298, 111.427
Angle α, β, γ (deg.)90.000, 93.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Monomeric sarcosine oxidase / MSOX


Mass: 43129.371 Da / Num. of mol.: 4 / Mutation: K256R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: B-0618 / 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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H2O

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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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 20% PEG4000, 200 mM sodium acetate, 100 mM Tris HCL, pH 8.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 83978 / % possible obs: 95.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21
Reflection shellResolution: 2→2.18 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.2 / % possible all: 96

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0066refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.609 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.268 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4212 5 %RANDOM
Rwork0.187 ---
obs0.19 83762 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.73 Å2 / Biso mean: 37.122 Å2 / Biso min: 10.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11912 0 226 497 12635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02212452
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.97316908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27551520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68124.138580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.715151984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0251560
X-RAY DIFFRACTIONr_chiral_restr0.140.21800
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219564
X-RAY DIFFRACTIONr_mcbond_it1.1231.57540
X-RAY DIFFRACTIONr_mcangle_it1.884212120
X-RAY DIFFRACTIONr_scbond_it3.07434912
X-RAY DIFFRACTIONr_scangle_it4.6244.54788
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 282 -
Rwork0.229 5276 -
all-5558 -
obs--86 %

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