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Basic information

Entry
Database: PDB / ID: 1ogp
TitleThe crystal structure of plant sulfite oxidase provides insight into sulfite oxidation in plants and animals
ComponentsSULFITE OXIDASE
KeywordsOXIDOREDUCTASE / MOLYBDENUM COFACTOR / MOLYBDOPTERIN / PLANT SULFITE OXIDASE / PEROXISOMES / INTRAMOLECULAR ELECTRON TRANSFER / OXIDOREDUCTAS
Function / homology
Function and homology information


response to sulfur dioxide / sulfite oxidase / chlorophyll metabolic process / sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / peroxisome / mitochondrion / cytosol
Similarity search - Function
Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Immunoglobulin E-set ...Immunoglobulin-like - #650 / Sulfite Oxidase; Chain A, domain 2 / Oxidoreductase, molybdopterin-binding domain / Moybdenum cofactor oxidoreductase, dimerisation / Eukaryotic molybdopterin oxidoreductase / Mo-co oxidoreductase dimerisation domain / Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / Immunoglobulin E-set / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / (MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(VI) / Sulfite oxidase
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSchrader, N. / Fischer, K. / Theis, K. / Mendel, R.R. / Schwarz, G. / Kisker, C.
CitationJournal: Structure / Year: 2003
Title: The Crystal Structure of Plant Sulfite Oxidase Provides Insights Into Sulfite Oxidation in Plants and Animals
Authors: Schrader, N. / Fischer, K. / Theis, K. / Mendel, R.R. / Schwarz, G. / Kisker, C.
History
DepositionMay 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SULFITE OXIDASE
B: SULFITE OXIDASE
C: SULFITE OXIDASE
D: SULFITE OXIDASE
E: SULFITE OXIDASE
F: SULFITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,53730
Polymers260,2876
Non-polymers5,25124
Water10,701594
1
A: SULFITE OXIDASE
B: SULFITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,51210
Polymers86,7622
Non-polymers1,7508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: SULFITE OXIDASE
D: SULFITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,51210
Polymers86,7622
Non-polymers1,7508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: SULFITE OXIDASE
F: SULFITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,51210
Polymers86,7622
Non-polymers1,7508
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)222.918, 351.271, 158.282
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11F-2033-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.28, 0.475, -0.834), (0.485, -0.68, -0.55), (-0.829, -0.558, -0.04)37.74294, 188.80194, 141.71674
2given(0.502, -0.854, 0.135), (-0.071, 0.115, 0.991), (-0.862, -0.507, -0.003)36.13667, 31.53868, 119.53288
3given(-0.658, 0.751, 0.049), (-0.752, -0.654, -0.082), (-0.029, -0.091, 0.995)-88.29889, 192.3714, -5.44752
4given(0.421, 0.907, 0.028), (0.907, -0.421, 0.019), (0.029, 0.017, -0.999)-104.59259, 160.97485, 84.87126
5given(0.31436, -0.43142, -0.84561), (-0.45483, 0.71342, -0.53307), (0.83325, 0.55219, 0.02805)85.66853, 117.62367, -53.16873
6given(-0.28, 0.475, -0.834), (0.485, -0.68, -0.55), (-0.829, -0.558, -0.04)37.74294, 188.80194, 141.71674
7given(0.502, -0.854, 0.135), (-0.071, 0.115, 0.991), (-0.862, -0.507, -0.003)36.13667, 31.53868, 119.53288
8given(-0.658, 0.751, 0.049), (-0.752, -0.654, -0.082), (-0.029, -0.091, 0.995)-88.29889, 192.3714, -5.44752
9given(0.421, 0.907, 0.028), (0.907, -0.421, 0.019), (0.029, 0.017, -0.999)-104.59259, 160.97485, 84.87126
10given(0.31436, -0.43142, -0.84561), (-0.45483, 0.71342, -0.53307), (0.83325, 0.55219, 0.02805)85.66853, 117.62367, -53.16873

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Components

#1: Protein
SULFITE OXIDASE / SOX / MOCO CONTAINING PROTEIN


Mass: 43381.098 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: ONE MOLYBDENUMN COFACTOR IN EACH MOLECULE / Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PQE80 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: Q9S850, sulfite oxidase
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cs
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MTQ / (MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(VI)


Mass: 517.243 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H8MoN5O8PS2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 5.7 Å3/Da / Density % sol: 78 %
Crystal growpH: 9.2
Details: 5-12% JEFFAMINE 600, 50 MM TRIS/HCL, 10 MM CSCL, PH 9.2
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 9.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115-60 mg/mlprotein1drop
25-12 %Jeffamine6001reservoir
350 mMTris-HCl1reservoir
410 mMCsCl1reservoirpH9.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2002 / Details: BENT CONICAL SI-MIRROR
RadiationMonochromator: BENT CYLINDRICAL GE(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 199819 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.6
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.03 / % possible all: 99.5
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Num. measured all: 1177360 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
BEASTphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SOX

1sox


Resolution: 2.6→182.57 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.893 / SU B: 8.128 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 9369 5 %RANDOM
Rwork0.235 ---
obs0.237 178219 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: 52.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---1.25 Å20 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.6→182.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18084 0 210 594 18888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.02118720
X-RAY DIFFRACTIONr_bond_other_d0.0040.0216842
X-RAY DIFFRACTIONr_angle_refined_deg2.6141.95525494
X-RAY DIFFRACTIONr_angle_other_deg1.775339252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40852322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1770.22796
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0220766
X-RAY DIFFRACTIONr_gen_planes_other0.010.023654
X-RAY DIFFRACTIONr_nbd_refined0.270.24100
X-RAY DIFFRACTIONr_nbd_other0.2720.220057
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1070.211937
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2860.2804
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.5560.214
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3190.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.453511604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.585618816
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.81567116
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1937.56678
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.381 750
Rwork0.343 13157
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.034
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.614
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg7.408

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