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- PDB-1l9e: Role of Histidine 269 in Catalysis by Monomeric Sarcosine Oxidase -

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Basic information

Entry
Database: PDB / ID: 1l9e
TitleRole of Histidine 269 in Catalysis by Monomeric Sarcosine Oxidase
ComponentsMonomeric sarcosine oxidase
KeywordsOXIDOREDUCTASE / flavoprotein / oxidase
Function / homology
Function and homology information


L-lysine catabolic process to acetyl-CoA via L-pipecolate / L-pipecolate oxidase activity / sarcosine oxidase (formaldehyde-forming) / 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 / IMIDAZOLE / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / refined directly / Resolution: 1.85 Å
AuthorsZhao, G. / Song, H. / Chen, Z.-w. / Mathews, F.S. / Jorns, M.S.
Citation
Journal: Biochemistry / Year: 2002
Title: Monomeric sarcosine oxidase: role of histidine 269 in catalysis.
Authors: Zhao, G. / Song, H. / 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 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,9838
Polymers86,2032
Non-polymers1,7806
Water8,233457
1
A: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9914
Polymers43,1011
Non-polymers8903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9914
Polymers43,1011
Non-polymers8903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.083, 70.638, 74.297
Angle α, β, γ (deg.)90.000, 93.78, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe biological assembly is monomer.

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Components

#1: Protein Monomeric sarcosine oxidase / E.C.1.5.3.1 / MSOX


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 / Production host: Escherichia coli (E. coli) / Strain (production host): DH1
References: UniProt: P40859, sarcosine oxidase (formaldehyde-forming)
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: phosphate, imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP at 295K, temperature 295.0K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
31.9-2.1 Msodium potassium phosphate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 12, 2001
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 64360 / Num. obs: 57602 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3 / Num. unique all: 3709 / % possible all: 57.7
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 57.7 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: refined directly
Starting model: PDB code 1B3M

1b3m
PDB Unreleased entry


Resolution: 1.85→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.195 5835 10.1 %RANDOM
Rwork0.168 ---
all-64549 --
obs-57663 89.3 %-
Displacement parametersBiso mean: 23.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6016 0 118 457 6591
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.85-1.960.25086870.225X-RAY DIFFRACTION70506
1.96-2.120.226810010.1846X-RAY DIFFRACTION97546
2.12-2.330.215110380.1764X-RAY DIFFRACTION99556
2.33-2.670.211310340.1782X-RAY DIFFRACTION101956
2.67-3.360.202910330.1732X-RAY DIFFRACTION103726
3.36-300.160710420.1452X-RAY DIFFRACTION103376
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Lowest resolution: 1.9 Å / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.251

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