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- PDB-2a9d: Crystal structure of recombinant chicken sulfite oxidase with Arg... -

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Basic information

Entry
Database: PDB / ID: 2a9d
TitleCrystal structure of recombinant chicken sulfite oxidase with Arg at residue 161
ComponentsSulfite Oxidase
KeywordsOXIDOREDUCTASE / sulfite oxidase / Molybdopterin / Molybdenum
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: 1.701 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 1.3Oct 20, 2021Group: 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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)82,83510
Polymers81,4682
Non-polymers1,3678
Water14,844824
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-108 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.137, 123.102, 55.129
Angle α, β, γ (deg.)90.00, 94.31, 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: 40733.965 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.: 824 / 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: 2.37 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, MES, Magnesium sulfate, 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: 1.25 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 77687 / % possible obs: 95.1 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.071 / Χ2: 1.535
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID
1.7-1.7673.31.60.38659751.2081
1.76-1.8391.11.90.32473741.3331
1.83-1.9197.62.20.24679411.3651
1.91-2.0298.22.20.17480311.4331
2.02-2.1498.32.20.13380101.6121
2.14-2.3198.32.20.10880051.5491
2.31-2.5498.92.20.09180961.5331
2.54-2.91992.20.07780811.6561
2.91-3.66992.20.0681101.7541
3.66-3097.52.20.04880641.6161

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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 Entry 1SOX

1sox


Resolution: 1.701→30 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.354 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 3913 5 %RANDOM
Rwork0.155 ---
all0.157 ---
obs0.157 77657 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.761 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.14 Å2
2--0.88 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.701→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5639 0 70 824 6533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225883
X-RAY DIFFRACTIONr_bond_other_d0.0020.025315
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9688061
X-RAY DIFFRACTIONr_angle_other_deg1.335312313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3855725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47622.239259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61515854
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3441562
X-RAY DIFFRACTIONr_chiral_restr0.0970.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026588
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021224
X-RAY DIFFRACTIONr_nbd_refined0.20.31116
X-RAY DIFFRACTIONr_nbd_other0.1980.35572
X-RAY DIFFRACTIONr_nbtor_refined0.1790.52797
X-RAY DIFFRACTIONr_nbtor_other0.0880.53456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.51107
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0980.53
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.325
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.3100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.545
X-RAY DIFFRACTIONr_mcbond_it1.19224599
X-RAY DIFFRACTIONr_mcbond_other0.21121454
X-RAY DIFFRACTIONr_mcangle_it1.3635888
X-RAY DIFFRACTIONr_scbond_it0.89522645
X-RAY DIFFRACTIONr_scangle_it1.32732173
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5341 / Refine-ID: X-RAY DIFFRACTION

RmsTypeWeight
0.42MEDIUM POSITIONAL0.5
0.46MEDIUM THERMAL2
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 204 -
Rwork0.256 4032 -
all-4236 -
obs--70.95 %
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)
10.37250.03810.00930.24240.16350.24560.02710.0248-0.0445-0.02880.0094-0.020.01360.0051-0.0366-0.0109-0.01020.0007-0.0223-0.0109-0.01732.39830.097918.1822
20.31770.04220.2270.26870.15450.7549-0.00380.01140.0474-0.0244-0.0078-0.0003-0.08310.09030.0117-0.0166-0.01990.0077-0.01-0.0046-0.01825.845826.280735.4599
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA100 - 4666 - 372
22BB110 - 46616 - 372

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