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- PDB-3qss: Crystal structure for the MSOX.chloride.MTA ternary complex -

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Basic information

Entry
Database: PDB / ID: 3qss
TitleCrystal structure for the MSOX.chloride.MTA ternary complex
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 / [METHYLTHIO]ACETATE / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKommoju, P. / Chen, Z. / Bruckner, R.C. / Mathews, F.S. / Jorns, M.S.
Citation
Journal: Biochemistry / Year: 2011
Title: Probing oxygen activation sites in two flavoprotein oxidases using chloride as an oxygen surrogate.
Authors: Kommoju, P.R. / Chen, Z.W. / Bruckner, R.C. / 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
DepositionFeb 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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)88,12610
Polymers86,2032
Non-polymers1,9238
Water9,512528
1
A: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0635
Polymers43,1011
Non-polymers9624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0635
Polymers43,1011
Non-polymers9624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.976, 69.478, 72.747
Angle α, β, γ (deg.)90.00, 92.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MTG / [METHYLTHIO]ACETATE


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


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.9 M Na/K phosphate, then the crystal was soaked with 12 mM MTA and 2.5 M NaCl, pH 7.0, VAPOR DIFFUSION, HANGING 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: Oct 27, 2008
RadiationMonochromator: APS Beamline 14-BM-C / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 60161 / Num. obs: 56973 / % possible obs: 94.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.85-1.9270.5493.75564192.6
1.92-1.9970.3545.85575193.9
1.99-2.0870.2567.95688194.7
2.08-2.197.20.18810.95746196
2.19-2.337.30.15113.45779196.7
2.33-2.517.40.1216.15796196.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPfrom ccp4phasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1L9F

1l9f
PDB Unreleased entry


Resolution: 1.85→29.73 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 326225.51 / 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
Rfree0.236 2713 5.1 %RANDOM
Rwork0.208 ---
obs0.208 53392 88.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.8738 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.18 Å20 Å2-5.01 Å2
2--11.74 Å20 Å2
3----5.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.85→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 0 122 528 6632
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.532
X-RAY DIFFRACTIONc_scbond_it1.642
X-RAY DIFFRACTIONc_scangle_it2.352.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 392 5.2 %
Rwork0.291 7195 -
obs-7195 75.6 %

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