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- PDB-1l9c: Role of Histidine 269 in Catalysis by Monomeric Sarcosine Oxidase -

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Basic information

Entry
Database: PDB / ID: 1l9c
TitleRole of Histidine 269 in Catalysis by Monomeric Sarcosine Oxidase
ComponentsMonomeric Sarcosine 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
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / refined directly / Resolution: 1.9 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 1.4Oct 27, 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 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 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)87,8927
Polymers86,1552
Non-polymers1,7375
Water19,1861065
1
A: Monomeric Sarcosine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8983
Polymers43,0771
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monomeric Sarcosine Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9934
Polymers43,0771
Non-polymers9163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.706, 69.245, 73.324
Angle α, β, γ (deg.)90.00, 94.25, 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: 43077.312 Da / Num. of mol.: 2 / Mutation: H269N
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


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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1065 / 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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: phosphate, 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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 18, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 57652 / Num. obs: 50561 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 7.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3011 / % possible all: 52.5
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.95 Å / % possible obs: 52.5 % / Rmerge(I) obs: 0.192

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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: 1.9→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
Rfree0.216 5114 10.1 %RANDOM
Rwork0.171 ---
all-57371 --
obs-50444 87.9 %-
Displacement parametersBiso mean: 17.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 113 1065 7190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
1.9-2.020.27325640.2233X-RAY DIFFRACTION55156
2.02-2.170.24158500.1926X-RAY DIFFRACTION82026
2.17-2.390.23168880.1826X-RAY DIFFRACTION87106
2.39-2.740.25318690.1794X-RAY DIFFRACTION91706
2.74-3.450.2169610.166X-RAY DIFFRACTION94206
3.45-25.140.17249820.1464X-RAY DIFFRACTION94276
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Lowest resolution: 1.95 Å / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.243

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