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- PDB-3bhf: Crystal structure of R49K mutant of Monomeric Sarcosine Oxidase c... -

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Basic information

Entry
Database: PDB / ID: 3bhf
TitleCrystal structure of R49K mutant of Monomeric Sarcosine Oxidase crystallized in PEG as precipitant
ComponentsMonomeric sarcosine oxidase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN OXIDASE / Cytoplasm / FAD
Function / homology
Function and homology information


sarcosine oxidase (formaldehyde-forming) / sarcosine oxidase activity / 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 / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHassan-Abdallah, A. / Zhao, G. / Chen, Z. / Mathews, F.S. / Jorns, M.S.
Citation
Journal: Biochemistry / Year: 2008
Title: Arginine 49 is a bifunctional residue important in catalysis and biosynthesis of monomeric sarcosine oxidase: a context-sensitive model for the electrostatic impact of arginine to lysine mutations.
Authors: Hassan-Abdallah, A. / Zhao, G. / Chen, Z.W. / Mathews, F.S. / Schuman Jorns, M.
#1: Journal: Structure / Year: 1999
Title: Monomeric Sarcosine Oxidase: Structure of a Covalently Flavinylated amine Oxidizing Enzyme
Authors: Trickey, P. / Wagner, M.A. / Jorns, M.S. / Mathews, F.S.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0516
Polymers86,4092
Non-polymers1,6424
Water6,305350
1
A: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0263
Polymers43,2051
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)44,0263
Polymers43,2051
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.348, 70.456, 79.595
Angle α, β, γ (deg.)90.00, 96.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Monomeric sarcosine oxidase / MSOX


Mass: 43204.535 Da / Num. of mol.: 2 / Mutation: R49K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Gene: soxA, sox / Production host: Escherichia coli (E. coli) / Strain (production host): DH1
References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 200 mM NaNO3, 20% PEG 3350, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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 / Date: Apr 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 46999 / Num. obs: 43803 / % possible obs: 93.2 % / Observed criterion σ(F): -0.9 / Observed criterion σ(I): -0.9 / Redundancy: 3.5 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2 / Num. unique all: 3448 / % possible all: 74

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L9F

1l9f
PDB Unreleased entry


Resolution: 2.1→39.52 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 179408.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2109 5 %RANDOM
Rwork0.202 ---
obs0.202 42142 90.4 %-
Displacement parametersBiso mean: 37.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 108 350 6434
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 276 5 %
Rwork0.332 5233 -
obs-5468 71.3 %

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