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- PDB-2a9b: Crystal structure of R138Q mutant of recombinant sulfite oxidase ... -

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Basic information

Entry
Database: PDB / ID: 2a9b
TitleCrystal structure of R138Q mutant of recombinant sulfite oxidase at resting state
ComponentsSulfite Oxidase
KeywordsOXIDOREDUCTASE / sulfite oxidase / molybdopterin / molybdenum / mutant / R160Q / R138Q
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: 2.503 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 / Derived calculations / 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.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.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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1324
Polymers40,6051
Non-polymers5273
Water3,873215
1
A: Sulfite Oxidase
hetero molecules

A: Sulfite Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2638
Polymers81,2102
Non-polymers1,0536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area4800 Å2
ΔGint-70 kcal/mol
Surface area28420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)86.109, 86.109, 153.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Cell settingtetragonal
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-2543-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis, 7_544

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Components

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


Mass: 40604.758 Da / Num. of mol.: 1
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 SpaceMitochondrion
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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#4: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 3.52 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, magnesium chloride, 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: Aug 20, 2003
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: 19275 / % possible obs: 100 % / Rmerge(I) obs: 0.089 / Χ2: 1.081
Reflection shellResolution: 2.5→2.59 Å / % possible obs: 100 % / Rmerge(I) obs: 0.599 / Num. measured obs: 1936 / Χ2: 1.052 / % possible all: 100

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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 2A99

2a99


Resolution: 2.503→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 11.74 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.202 947 4.9 %Copied from R-free of reflections of wild type crystals (PDB Entry 2A99)
Rwork0.156 ---
all0.158 ---
obs0.158 19258 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.854 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å20 Å20 Å2
2--1.7 Å20 Å2
3----3.4 Å2
Refinement stepCycle: LAST / Resolution: 2.503→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 26 215 3110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222983
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9674089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7175371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.2822.443131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8715428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1541530
X-RAY DIFFRACTIONr_chiral_restr0.090.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022362
X-RAY DIFFRACTIONr_nbd_refined0.220.31297
X-RAY DIFFRACTIONr_nbtor_refined0.3280.51993
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.5351
X-RAY DIFFRACTIONr_metal_ion_refined0.1980.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.518
X-RAY DIFFRACTIONr_mcbond_it0.7241.51893
X-RAY DIFFRACTIONr_mcangle_it1.3123006
X-RAY DIFFRACTIONr_scbond_it1.69231257
X-RAY DIFFRACTIONr_scangle_it2.934.51083
LS refinement shellResolution: 2.503→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 65 -
Rwork0.241 1354 -
all-1419 -
obs--98.06 %
Refinement TLS params.Method: refined / Origin x: 3.208 Å / Origin y: 0.169 Å / Origin z: 18.262 Å
111213212223313233
T-0.0028 Å20.0068 Å2-0.0027 Å2--0.0101 Å2-0.0078 Å2---0.0227 Å2
L0.3235 °2-0.0136 °2-0.2441 °2-0.1905 °2-0.0636 °2--0.222 °2
S-0.0597 Å °0.0745 Å °-0.0788 Å °-0.0008 Å °0.022 Å °0.0829 Å °-0.0148 Å °-0.0227 Å °0.0376 Å °
Refinement TLS groupSelection: ALL

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