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- PDB-2a9c: Crystal structure of R138Q mutant of recombinant chicken sulfite ... -

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Basic information

Entry
Database: PDB / ID: 2a9c
TitleCrystal structure of R138Q mutant of recombinant chicken sulfite oxidase with the bound product, sulfate, at the active site
ComponentsSulfite Oxidase
KeywordsOXIDOREDUCTASE / sulfite oxidase / Molybdopterin / Molybdenum / CSO / sulfate / R138Q / R160Q
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 / FOURIER SYNTHESIS / Resolution: 2.505 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)82,4769
Polymers81,2102
Non-polymers1,2677
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-84 kcal/mol
Surface area27450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.905, 122.572, 55.180
Angle α, β, γ (deg.)90.00, 94.97, 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 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 108 - 466 / Label seq-ID: 14 - 372

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe asymmetric unit contains a dimer which is the functional unit

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 40604.758 Da / Num. of mol.: 2
Fragment: Catalytic core domain and C terminal dimerization domain
Mutation: R138Q
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

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Non-polymers , 5 types, 539 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 46.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, Magnesium sulfate, HEPES, pH 7.0, 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: Aug 24, 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: 2.5→30 Å / Num. obs: 23882 / % possible obs: 97.7 % / Rmerge(I) obs: 0.157 / Χ2: 1.221
Reflection shell
Resolution (Å)% possible obs (%)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID
2.5-2.5997.30.5223611.0991
2.59-2.6996.30.46923461.2121
2.69-2.8297.20.37323611.1191
2.82-2.9697.70.29323931.1711
2.96-3.1598.10.22323661.1661
3.15-3.3997.90.16324071.2721
3.39-3.73970.12923631.3641
3.73-4.2797.80.10523941.4081
4.27-5.3898.80.08624391.2761
5.38-3098.50.07824521.1271

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
REFMAC5.2refinement
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2A9A

2a9a


Resolution: 2.505→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.863 / SU B: 16.673 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1215 5.1 %Copied from Rfree reflections of wild type protein crystals (PDB Entry 2A9A)
Rwork0.156 ---
all0.16 ---
obs0.16 23858 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.601 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20.45 Å2
2---0.14 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.505→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 66 532 6142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225773
X-RAY DIFFRACTIONr_bond_other_d0.0020.025218
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9677909
X-RAY DIFFRACTIONr_angle_other_deg1.171312090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0945716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50622.46252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9515838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0811558
X-RAY DIFFRACTIONr_chiral_restr0.0950.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026486
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021194
X-RAY DIFFRACTIONr_nbd_refined0.20.31179
X-RAY DIFFRACTIONr_nbd_other0.1960.35518
X-RAY DIFFRACTIONr_nbtor_refined0.1860.52774
X-RAY DIFFRACTIONr_nbtor_other0.0930.53570
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.5720
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0060.51
X-RAY DIFFRACTIONr_metal_ion_refined0.2370.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.379
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3250.517
X-RAY DIFFRACTIONr_mcbond_it0.94924467
X-RAY DIFFRACTIONr_mcbond_other0.1321440
X-RAY DIFFRACTIONr_mcangle_it1.14535794
X-RAY DIFFRACTIONr_scbond_it0.54922578
X-RAY DIFFRACTIONr_scangle_it0.84932115
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5365 / Refine-ID: X-RAY DIFFRACTION

RmsTypeWeight
0.34MEDIUM POSITIONAL0.5
0.41MEDIUM THERMAL2
LS refinement shellResolution: 2.505→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 89 -
Rwork0.234 1550 -
all-1639 -
obs--91.21 %
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)
10.9277-0.1575-0.0260.31690.06540.38090.01350.0362-0.0287-0.0285-0.0097-0.00470.01510.006-0.0038-0.0072-0.00130.001-0.022-0.0063-0.04473.14470.522918.4537
20.88230.03160.23120.38360.06940.6315-0.0208-0.01740.0498-0.0059-0.0203-0.0198-0.0726-0.01060.04110.0018-0.00490.0116-0.0294-0.0031-0.03083.975926.467735.5427
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 108 - 466 / Label seq-ID: 14 - 372

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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