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- PDB-3r19: Chicken sulfite oxidase triple mutant with altered activity and s... -

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Basic information

Entry
Database: PDB / ID: 3r19
TitleChicken sulfite oxidase triple mutant with altered activity and substrate affinity
ComponentsSulfite oxidase
KeywordsOXIDOREDUCTASE / molybdenum / molybdopterin / oxotransferase / sulfite oxidase / nitrate reductase / metal binding / nitrogen assimilation
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: 2.1 Å
AuthorsQiu, J.A.
CitationJournal: Biochemistry / Year: 2012
Title: Structure-based alteration of substrate specificity and catalytic activity of sulfite oxidase from sulfite oxidation to nitrate reduction.
Authors: Qiu, J.A. / Wilson, H.L. / Rajagopalan, K.V.
History
DepositionMar 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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_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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4493
Polymers50,9581
Non-polymers4912
Water3,423190
1
A: Sulfite oxidase
hetero molecules

A: Sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8996
Polymers101,9162
Non-polymers9834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
Buried area4660 Å2
ΔGint-47 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.599, 85.599, 152.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Sulfite oxidase


Mass: 50958.184 Da / Num. of mol.: 1 / Fragment: rCSO (UNP residues 95-466) / Mutation: Y332N, R450M, V452M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SULFITE OXIDASE, SUOX / Plasmid: PTRC99A RCSO 3NR / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 / References: UniProt: P07850, sulfite oxidase
#2: 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
#3: Chemical ChemComp-MO / MOLYBDENUM ATOM


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


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE UNIPROT SEQUENCE FOR P07850 CONTAINS A NUMBER OF ENTRIES THAT WERE CORRECTED IN PDB ENTRY 1SOX. ...THE UNIPROT SEQUENCE FOR P07850 CONTAINS A NUMBER OF ENTRIES THAT WERE CORRECTED IN PDB ENTRY 1SOX. THE CLONED GENE USED IN THIS STUDY HAS THE SAME CORRECTIONS AS REPORTED IN KARAKAS ET AL. J BIOL CHEM. 2005 SEP 30;280(39):33506-15.

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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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15 % PEG 6000 (W/V), 5 % MPD (V/V), 100 mM MES pH 6.5, and 2% (w/v) benzamidine hydrochloride hydrate, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2008
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→47.46 Å / Num. all: 31937 / Num. obs: 31937 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.103 / Net I/σ(I): 39.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.288 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A99

2a99


Resolution: 2.1→47.46 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 6.631 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.149 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1610 5 %RANDOM
Rwork0.167 ---
all0.237 30282 --
obs0.169 30282 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.777 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å2-0 Å2-0 Å2
2--1.18 Å20 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 25 190 3080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222988
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.9684094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8685373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55622.519131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.61215436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1311530
X-RAY DIFFRACTIONr_chiral_restr0.0730.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222364
X-RAY DIFFRACTIONr_mcbond_it0.441.51865
X-RAY DIFFRACTIONr_mcangle_it0.84223012
X-RAY DIFFRACTIONr_scbond_it1.46931123
X-RAY DIFFRACTIONr_scangle_it2.4294.51081
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 120 -
Rwork0.237 2140 -
obs--95.6 %
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)
10.8409-0.3044-0.12031.56910.39811.99740.01840.0365-0.12570.0577-0.09560.1150.4515-0.16920.07720.1475-0.07180.00670.1274-0.04020.0572.0517.9314.834
20.9292-0.16350.64031.63620.64713.237-0.0569-0.0421-0.01750.1675-0.0322-0.02330.2289-0.04910.08910.0964-0.02090.01430.1454-0.01930.04384.65625.0712.07
30.3566-0.2732-0.11591.4403-0.19922.14910.04270.1278-0.004-0.2258-0.1177-0.08110.23350.11820.0750.0886-0.00160.01450.1904-0.01960.05855.32630.58-3.29
43.742-1.41393.25523.0347-1.68817.46660.0609-0.0821-0.2416-0.27120.08310.70150.2139-0.5579-0.1440.0517-0.0208-0.06780.2909-0.03270.1786-13.66738.051-6.332
51.35-0.8018-0.69982.2119-0.13072.14380.15410.3673-0.109-0.5359-0.1650.26330.2687-0.40140.01090.162-0.0118-0.06070.286-0.05120.0374-7.03633.752-13.186
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A95 - 199
2X-RAY DIFFRACTION2A200 - 303
3X-RAY DIFFRACTION3A304 - 377
4X-RAY DIFFRACTION4A378 - 406
5X-RAY DIFFRACTION5A407 - 466

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