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- PDB-1el5: COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR DIMETHY... -

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Basic information

Entry
Database: PDB / ID: 1el5
TitleCOMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR DIMETHYLGLYCINE
ComponentsSARCOSINE OXIDASE
KeywordsOXIDOREDUCTASE / flavoprotein / 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 / 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
N,N-DIMETHYLGLYCINE / FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsWagner, M.A. / Trickey, P. / Chen, Z.-W. / Mathews, F.S. / Jorns, M.S.
Citation
Journal: Biochemistry / Year: 2000
Title: Monomeric sarcosine oxidase: 1. Flavin reactivity and active site binding determinants.
Authors: Wagner, M.A. / Trickey, P. / Chen, Z.W. / Mathews, F.S. / Jorns, M.S.
#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
DepositionMar 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SARCOSINE OXIDASE
B: SARCOSINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,33611
Polymers86,2032
Non-polymers2,1339
Water14,124784
1
A: SARCOSINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1205
Polymers43,1011
Non-polymers1,0194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SARCOSINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2156
Polymers43,1011
Non-polymers1,1145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.865, 69.503, 73.498
Angle α, β, γ (deg.)90.00, 94.25, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is monomer.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SARCOSINE OXIDASE


Mass: 43101.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: B-0618 / Cell (production host): DH1 CELLS / Production host: Escherichia coli (E. coli)
References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming)

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Non-polymers , 5 types, 793 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-DMG / N,N-DIMETHYLGLYCINE / DIMETHYLGLYCINE


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 784 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: phosphate, tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K
Crystal grow
*PLUS
pH: 8
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
220 mMTris-HCl1drop
32.1 Msodium/potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→500 Å / Num. all: 68112 / Num. obs: 60143 / % possible obs: 88.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.333 / Num. unique all: 1247 / % possible all: 36.7
Reflection shell
*PLUS
% possible obs: 36.7 %

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNS0.9refinement
RefinementResolution: 1.8→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.208 5857 -RANDOM
Rwork0.165 ---
obs0.165 58630 86.3 %-
all-67941 --
Refinement stepCycle: LAST / Resolution: 1.8→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6016 0 137 784 6937
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.81
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg

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