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- PDB-1x31: Crystal Structure of Heterotetrameric Sarcosine Oxidase from Cory... -

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Basic information

Entry
Database: PDB / ID: 1x31
TitleCrystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96
Components(Sarcosine oxidase ...) x 4
KeywordsOXIDOREDUCTASE / Heterotetrameric sarcosine oxidase / flavoenzyme
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
N,N-DIMETHYLGLYCINE / FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Sarcosine oxidase subunit gamma / Sarcosine oxidase subunit alpha / Sarcosine oxidase subunit delta / Sarcosine oxidase subunit beta
Similarity search - Component
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsIda, K. / Moriguchi, T. / Suzuki, H.
CitationJournal: BIOCHEM.BIOPHYS.RES.COMMUN. / Year: 2005
Title: Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96
Authors: Ida, K. / Moriguchi, T. / Suzuki, H.
History
DepositionApr 27, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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)182,92017
Polymers180,0774
Non-polymers2,84213
Water20,4291134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21660 Å2
ΔGint-177 kcal/mol
Surface area55020 Å2
MethodPISA
2
A: Sarcosine oxidase alpha subunit
B: Sarcosine oxidase beta subunit
C: Sarcosine oxidase gamma subunit
D: Sarcosine oxidase delta subunit
hetero molecules

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)365,83934
Polymers360,1558
Non-polymers5,68526
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area46210 Å2
ΔGint-367 kcal/mol
Surface area107160 Å2
MethodPISA
3
A: Sarcosine oxidase alpha subunit
B: Sarcosine oxidase beta subunit
C: Sarcosine oxidase gamma subunit
D: Sarcosine oxidase delta subunit
hetero molecules

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)365,83934
Polymers360,1558
Non-polymers5,68526
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area45690 Å2
ΔGint-371 kcal/mol
Surface area107670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.112, 199.112, 197.205
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-3557-

HOH

21A-4078-

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. (bacteria) / Strain: U-96 / Plasmid: pET31b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q50LF0, sarcosine oxidase (formaldehyde-forming)
#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. (bacteria) / Strain: U-96 / Plasmid: pET31b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q50LF2, sarcosine oxidase (formaldehyde-forming)
#3: Protein Sarcosine oxidase gamma subunit


Mass: 21732.541 Da / Num. of mol.: 1 / Fragment: residues 1-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Strain: U-96 / Plasmid: pET31b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q50LE9, sarcosine oxidase (formaldehyde-forming)
#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. (bacteria) / Strain: U-96 / Plasmid: pET31b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q50LF1, sarcosine oxidase (formaldehyde-forming)

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Non-polymers , 7 types, 1147 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#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-DMG / N,N-DIMETHYLGLYCINE / DIMETHYLGLYCINE


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#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.: 1134 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1M Tris-HCl, 1.9M ammonium sulfate, 10mM CuSO4, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11.00817
SYNCHROTRONPhoton Factory AR-NW12A21.00868, 1.00934, 1.02000
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 26, 2004
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.008171
21.008681
31.009341
41.021
ReflectionResolution: 2.15→70.06 Å / Num. obs: 124207 / % possible obs: 99.8 % / Redundancy: 10.3 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.092
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.319 / Num. unique all: 17623 / % possible all: 98.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→70.06 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 5651970.42 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 12401 10 %RANDOM
Rwork0.188 ---
obs0.188 124087 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.9327 Å2 / ksol: 0.372631 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.15→70.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12504 0 176 1134 13814
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.791
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.941.5
X-RAY DIFFRACTIONc_mcangle_it3.72
X-RAY DIFFRACTIONc_scbond_it4.52
X-RAY DIFFRACTIONc_scangle_it5.762.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 1986 9.9 %
Rwork0.217 18149 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2fadfmnnad-PRODRG.paramfadfmnnad-PRODRG.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5dmg.paramdmg.top

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