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- PDB-2a9a: Crystal structure of recombinant chicken sulfite oxidase with the... -

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Basic information

Entry
Database: PDB / ID: 2a9a
TitleCrystal structure of recombinant chicken sulfite oxidase with the bound product, sulfate, at the active site
ComponentsSulfite Oxidase
KeywordsOXIDOREDUCTASE / sulfite oxidase / Molybdopterin / Molybdenum / CSO / sulfate
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. / 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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MOLYBDENUM ATOM / Chem-MTE / Sulfite oxidase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsKarakas, E. / Wilson, H.L. / Graf, T.N. / Xiang, S. / Jaramillo-Busquets, S. / Rajagopalan, K.V. / Kisker, C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural insights into sulfite oxidase deficiency
Authors: Karakas, E. / Wilson, H.L. / Graf, T.N. / Xiang, S. / Jaramillo-Busquets, S. / Rajagopalan, K.V. / Kisker, C.
History
DepositionJul 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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_ncs_dom_lim / 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_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.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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Sulfite Oxidase
B: Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,63410
Polymers81,2682
Non-polymers1,3678
Water11,854658
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-107 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.001, 123.170, 55.482
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEUAA107 - 46613 - 372
2ARGARGBB108 - 46614 - 372
DetailsThe asymmetric unit contains a dimer which is the functional unit

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Components

#1: Protein Sulfite Oxidase / E.C.1.8.3.1


Mass: 40633.824 Da / Num. of mol.: 2
Fragment: Catalytic core domain and C terminal dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken)
Description: The gene is chemically synthesized based on the protein sequence of sulfite oxidase from Gallus gallus
Cellular location: Mitochondrial Intermembrane Space / Gene: SUOX / Organ: Liver / Organelle: Mitochondrion / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 / References: UniProt: P07850, sulfite oxidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 2.3 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, Magnesium sulfate, MES , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 48006 / % possible obs: 99.2 % / Rmerge(I) obs: 0.105 / Χ2: 1.013
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID
2-2.0792.80.55344681.2511
2.07-2.1599.90.46448261.2071
2.15-2.2599.60.33147771.1411
2.25-2.3799.90.2848311.0251
2.37-2.521000.19848340.8491
2.52-2.711000.16848300.9491
2.71-2.991000.11448480.8981
2.99-3.421000.07848210.9481
3.42-4.311000.06448551.0331
4.31-301000.04849160.9641

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Phasing

Phasing MRRfactor: 0.38 / Cor.coef. Fo:Fc: 0.6
Highest resolutionLowest resolution
Rotation3 Å38.26 Å
Translation3 Å38.26 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
REFMAC5.2refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID is 2A99

2a99


Resolution: 2.003→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.351 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2419 5 %RANDOM
Rwork0.159 ---
all0.162 ---
obs0.162 47924 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.989 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20.32 Å2
2--0.12 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.003→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5637 0 70 658 6365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225875
X-RAY DIFFRACTIONr_bond_other_d0.0020.025308
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9698051
X-RAY DIFFRACTIONr_angle_other_deg1.16312295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5255728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07822.266256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35315848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6951561
X-RAY DIFFRACTIONr_chiral_restr0.1080.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026597
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021222
X-RAY DIFFRACTIONr_nbd_refined0.1970.31046
X-RAY DIFFRACTIONr_nbd_other0.1970.35363
X-RAY DIFFRACTIONr_nbtor_refined0.1780.52738
X-RAY DIFFRACTIONr_nbtor_other0.0890.53499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.5812
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1050.52
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.330
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.3113
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.527
X-RAY DIFFRACTIONr_mcbond_it1.151.54601
X-RAY DIFFRACTIONr_mcbond_other0.2041.51462
X-RAY DIFFRACTIONr_mcangle_it1.31225894
X-RAY DIFFRACTIONr_scbond_it1.99432641
X-RAY DIFFRACTIONr_scangle_it2.8864.52157
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5371 / Refine-ID: X-RAY DIFFRACTION

RmsTypeWeight
0.34MEDIUM POSITIONAL0.5
0.52MEDIUM THERMAL2
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 148 -
Rwork0.241 2981 -
all-3129 -
obs--87.01 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.662-0.1296-0.01580.24990.07430.28070.04060.0334-0.0522-0.0096-0.0322-0.0030.01340.009-0.0083-0.02040.0002-0.0024-0.0274-0.008-0.03363.15410.115818.1898
20.66310.05370.14680.28610.15850.5108-0.0079-0.01540.0687-0.014-0.0316-0.0132-0.0535-0.00320.0395-0.0158-0.00550.0068-0.04-0.0041-0.02374.021526.575435.7791
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA96 - 4662 - 372
22BB108 - 46614 - 372

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