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- PDB-2gb0: Monomeric sarcosine oxidase: structure of a covalently flavinylat... -

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Basic information

Entry
Database: PDB / ID: 2gb0
TitleMonomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme
ComponentsMonomeric sarcosine oxidase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN OXIDASE
Function / homology
Function and homology information


sarcosine oxidase (formaldehyde-forming) / sarcosine oxidase activity / 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 / PHOSPHATE ION / Monomeric sarcosine oxidase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.85 Å
AuthorsTrickey, P. / Wagner, M.A. / Jorns, M.S. / Mathews, F.S.
CitationJournal: 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 9, 2006Deposition site: RCSB / Processing site: RCSB
SupersessionMar 21, 2006ID: 1L9F
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 9, 2024Group: 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: Monomeric sarcosine oxidase
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,22510
Polymers86,2032
Non-polymers2,0228
Water12,088671
1
A: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0174
Polymers43,1011
Non-polymers9163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Monomeric sarcosine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2076
Polymers43,1011
Non-polymers1,1065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.562, 69.555, 74.117
Angle α, β, γ (deg.)90.00, 94.26, 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: PHOSPHATE, VAPOR DIFFUSION, SITTING DROP AT 298K, pH 6.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 0.9792, 0.9794, 0.9392, 1.0679
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 8, 1998
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
30.93921
41.06791
ReflectionResolution: 1.85→43 Å / Num. all: 62740 / Num. obs: 58976 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 1.5 / % possible all: 57.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
DMmodel building
CNS1.1refinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→42.53 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 947266.85 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 5908 10.2 %RANDOM
Rwork0.165 ---
all-62923 --
obs-58044 92.1 %-
Displacement parametersBiso mean: 28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.85→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6064 0 128 671 6863
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
1.85-1.960.30636570.269X-RAY DIFFRACTION5803
1.96-2.120.230510250.1876X-RAY DIFFRACTION8837
2.12-2.330.20999950.1594X-RAY DIFFRACTION9320
2.33-2.670.219310730.1649X-RAY DIFFRACTION9285
2.67-3.360.207411100.1622X-RAY DIFFRACTION9355
3.36-42.530.165310480.1533X-RAY DIFFRACTION9536

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