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- PDB-1el9: COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYL... -

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Basic information

Entry
Database: PDB / ID: 1el9
TitleCOMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYLTHIO]ACETATE
ComponentsSARCOSINE OXIDE
KeywordsOXIDOREDUCTASE / flavoprotein / oxidase
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 / [METHYLTHIO]ACETATE / PHOSPHATE ION / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,99611
Polymers86,8592
Non-polymers2,1379
Water9,944552
1
A: SARCOSINE OXIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4515
Polymers43,4301
Non-polymers1,0214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SARCOSINE OXIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5466
Polymers43,4301
Non-polymers1,1165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.762, 69.587, 73.765
Angle α, β, γ (deg.)90.00, 94.02, 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 OXIDE


Mass: 43429.617 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, 561 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-MTG / [METHYLTHIO]ACETATE


Mass: 105.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Description: MAD phasing was not used to solve 1EL9 and 1ELI, but rather direct refinement as the crystals were isomorphous enough to the native crystals for phasing. Selenomethionine crystals were ...Description: MAD phasing was not used to solve 1EL9 and 1ELI, but rather direct refinement as the crystals were isomorphous enough to the native crystals for phasing. Selenomethionine crystals were used for the experiments since they were the only ones on hand at the time. Kinetic studies showed that the presence of selenomethionine had little effect.
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: Jul 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→500 Å / Num. all: 49552 / Num. obs: 43804 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.55 % / Rmerge(I) obs: 0.25 / Num. unique all: 2639 / % possible all: 53.6
Reflection shell
*PLUS
% possible obs: 53.6 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
SCALEPACKdata scaling
RefinementResolution: 2→500 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4474 -RANDOM
Rwork0.174 ---
obs0.174 43663 87.6 %-
all-49828 --
Refinement stepCycle: LAST / Resolution: 2→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6016 0 135 552 6703
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.68
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.311 / Rfactor Rwork: 0.278

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