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- PDB-3ad8: Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 ... -

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Basic information

Entry
Database: PDB / ID: 3ad8
TitleHeterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with pyrrole 2-carboxylate
Components(SARCOSINE OXIDASE ...) x 4
KeywordsOXIDOREDUCTASE / Sarcosine Oxidase / Ligand Complex
Function / homology
Function and homology information


sarcosine oxidase (5,10-methylenetetrahydrofolate-forming) / sarcosine catabolic process / sarcosine oxidase activity / tetrahydrofolate metabolic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Folate-binding fold / Folate-binding superfamily / Heterotetrameric sarcosine oxidase / Sarcosine oxidase, alpha subunit / Sarcosine oxidase subunit beta / Sarcosine oxidase, delta subunit, heterotetrameric / Sarcosine oxidase, gamma subunit, heterotetrameric / Sarcosine oxidase, gamma subunit / Sarcosine oxidase subunit delta superfamily / Sarcosine oxidase, delta subunit family ...Folate-binding fold / Folate-binding superfamily / Heterotetrameric sarcosine oxidase / Sarcosine oxidase, alpha subunit / Sarcosine oxidase subunit beta / Sarcosine oxidase, delta subunit, heterotetrameric / Sarcosine oxidase, gamma subunit, heterotetrameric / Sarcosine oxidase, gamma subunit / Sarcosine oxidase subunit delta superfamily / Sarcosine oxidase, delta subunit family / Sarcosine oxidase, gamma subunit family / SoxA, A3 domain / 2Fe-2S iron-sulfur cluster binding domain, N-terminal / Sarcosine oxidase A3 domain / FAD dependent oxidoreductase / Glycine cleavage T-protein, C-terminal barrel domain / Glycine cleavage T-protein C-terminal barrel domain / Glycine cleavage T-protein/YgfZ, C-terminal / Probable tRNA modification gtpase trme; domain 1 / Aminomethyltransferase-like / Aminomethyltransferase, folate-binding domain / Aminomethyltransferase folate-binding domain / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / Rhodanese-like domain / Gyrase A; domain 2 / 2Fe-2S iron-sulfur cluster binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PYRROLE-2-CARBOXYLATE / Sarcosine oxidase subunit gamma / Sarcosine oxidase subunit alpha / Sarcosine oxidase subunit delta / Sarcosine oxidase subunit beta
Similarity search - Component
Biological speciesCorynebacterium sp. U-96 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSuzuki, H. / Moriguchi, T. / Ida, K.
CitationJournal: J.Biochem. / Year: 2010
Title: Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96.
Authors: Moriguchi, T. / Ida, K. / Hikima, T. / Ueno, G. / Yamamoto, M. / Suzuki, H.
History
DepositionJan 15, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: SARCOSINE OXIDASE ALPHA SUBUNIT
B: SARCOSINE OXIDASE BETA SUBUNIT
C: SARCOSINE OXIDASE GAMMA SUBUNIT
D: SARCOSINE OXIDASE DELTA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,00521
Polymers179,7724
Non-polymers3,23417
Water18,3751020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16380 Å2
ΔGint-43 kcal/mol
Surface area56020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.796, 198.796, 196.819
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1161-

HOH

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Components

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SARCOSINE OXIDASE ... , 4 types, 4 molecules ABCD

#1: Protein SARCOSINE OXIDASE ALPHA SUBUNIT


Mass: 102850.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. U-96 (bacteria) / Gene: soxA / Plasmid: PET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50LF0
#2: Protein SARCOSINE OXIDASE BETA SUBUNIT


Mass: 44048.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. U-96 (bacteria) / Gene: soxB / Plasmid: PET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q50LF2, sarcosine oxidase (formaldehyde-forming)
#3: Protein SARCOSINE OXIDASE GAMMA SUBUNIT


Mass: 21427.186 Da / Num. of mol.: 1 / Fragment: UNP residues 11-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. U-96 (bacteria) / Gene: soxG / Plasmid: PET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50LE9
#4: Protein SARCOSINE OXIDASE DELTA SUBUNIT


Mass: 11445.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. U-96 (bacteria) / Gene: soxD / Plasmid: PET31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50LF1

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Non-polymers , 7 types, 1037 molecules

#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#8: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#9: Chemical ChemComp-PYC / PYRROLE-2-CARBOXYLATE


Mass: 110.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4NO2
#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1020 / 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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS-HCL, 1.9M AMMONIUM SULFATE, 10MM CUSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.00817 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00817 Å / Relative weight: 1
ReflectionResolution: 2.2→61.78 Å / Num. obs: 115711 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 8.1 / Rsym value: 0.233 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X31

1x31


Resolution: 2.2→61.31 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.847 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20606 5799 5 %RANDOM
Rwork0.16102 ---
obs0.16326 109866 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.783 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→61.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12519 0 197 1020 13736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02212981
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.851.96317695
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95651649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78623.783571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.301151988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4551593
X-RAY DIFFRACTIONr_chiral_restr0.1450.21985
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219939
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0051.58182
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.789213067
X-RAY DIFFRACTIONr_scbond_it3.2234799
X-RAY DIFFRACTIONr_scangle_it4.8244.54628
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 413 -
Rwork0.173 8041 -
obs--100 %

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