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- PDB-1sox: SULFITE OXIDASE FROM CHICKEN LIVER -

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Basic information

Entry
Database: PDB / ID: 1sox
TitleSULFITE OXIDASE FROM CHICKEN LIVER
ComponentsSULFITE OXIDASE
KeywordsOXIDOREDUCTASE / SULFITE OXIDATION
Function / homology
Function and homology information


sulfite oxidase / sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / mitochondrial intermembrane space / heme binding / mitochondrion
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 / Oxidoreductase, molybdopterin binding site ...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 / Oxidoreductase, molybdopterin binding site / Eukaryotic molybdopterin oxidoreductases signature. / Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / Immunoglobulin E-set / Roll / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / MOLYBDENUM ATOM / Chem-MTE / Sulfite oxidase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsKisker, C. / Schindelin, H. / Rees, D.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase.
Authors: Kisker, C. / Schindelin, H. / Pacheco, A. / Wehbi, W.A. / Garrett, R.M. / Rajagopalan, K.V. / Enemark, J.H. / Rees, D.C.
History
DepositionDec 31, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_asym_id / _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_asym_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_asym_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_asym_id / _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_asym_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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,93314
Polymers102,0022
Non-polymers2,93012
Water14,808822
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-143 kcal/mol
Surface area37010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.117, 197.690, 56.009
Angle α, β, γ (deg.)90.00, 94.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9996, -0.00587, -0.02773), (0.01586, -0.92662, -0.37566), (-0.02349, -0.37595, 0.92634)
Vector: 23.25864, 168.62854, 33.55973)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SULFITE OXIDASE /


Mass: 51001.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INTERMEMBRANE SPACEMitochondrion
Organ: LIVER / Organelle: MITOCHONDRION / References: UniProt: P07850, sulfite oxidase

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Non-polymers , 7 types, 834 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#4: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION USING HANGING DROPS AND USING MICROSEEDING. RESERVOIR: 0.65-0.9 M LI2SO4, 100 MM HEPES PH 7.5, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
20.65-0.9 M1reservoirLi2SO4
3100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 84147 / % possible obs: 89.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.06 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 1.8 % / Rsym value: 0.16 / % possible all: 66.2
Reflection
*PLUS
Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 66.2 % / Rmerge(I) obs: 0.16

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
Details: REFINEMENT WAS CARRIED OUT USING BOTH X-PLOR AND REFMAC.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2064 2.5 %RANDOM
Rwork0.1748 ---
obs0.1748 84147 89.2 %-
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.641 Å20 Å20.435 Å2
2---4.339 Å20 Å2
3---1.698 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7129 0 177 822 8128
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.432
X-RAY DIFFRACTIONx_mcangle_it3.223
X-RAY DIFFRACTIONx_scbond_it2.762
X-RAY DIFFRACTIONx_scangle_it3.93
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2441 235 2.5 %
Rwork0.205 9093 -
obs--79.97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2202
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rwork: 0.205

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