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- PDB-3r18: Chicken sulfite oxidase double mutant with altered activity and s... -

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Basic information

Entry
Database: PDB / ID: 3r18
TitleChicken sulfite oxidase double mutant with altered activity and substrate affinity
ComponentsSulfite oxidase
KeywordsOXIDOREDUCTASE / molybdenum / molybdopterin / sulfite oxidase / nitrate reductase / oxotransferase / 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: 2.4 Å
AuthorsQiu, J.A. / Wilson, H.L. / Rajagopalan, K.V.
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 1.1Feb 29, 2012Group: 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 / pdbx_struct_special_symmetry / 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)51,4173
Polymers50,9261
Non-polymers4912
Water3,567198
1
A: Sulfite oxidase
hetero molecules

A: Sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8356
Polymers101,8522
Non-polymers9834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4560 Å2
ΔGint-47 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.623, 85.623, 153.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-551-

HOH

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Components

#1: Protein Sulfite oxidase /


Mass: 50926.117 Da / Num. of mol.: 1 / Fragment: rCSO 2NR residues 94-466 / Mutation: Y322N, R450M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SULFITE OXIDASE, SUOX / Plasmid: PTRC99A RCSO 2NR / 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 / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG 10,000 (W/V), 10 mM barium chloride dihydrate, 100 mM ammonium acetate, 100 mM bis-TRIS propane pH 5.5, 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: 2.4→47.51 Å / Num. all: 21499 / Num. obs: 21499 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.099 / Net I/σ(I): 23.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.16 / Rsym value: 0.345 / % possible all: 96.9

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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: 2.4→47.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.152 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.252 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1098 5.1 %RANDOM
Rwork0.165 ---
all0.269 20379 --
obs0.167 20379 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: 34.458 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å2-0 Å2-0 Å2
2--0.86 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 25 198 3096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222998
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9664109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.995374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89622.5132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60515435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.611530
X-RAY DIFFRACTIONr_chiral_restr0.0780.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222374
X-RAY DIFFRACTIONr_mcbond_it0.4921.51870
X-RAY DIFFRACTIONr_mcangle_it0.97123021
X-RAY DIFFRACTIONr_scbond_it1.62931128
X-RAY DIFFRACTIONr_scangle_it2.7464.51087
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 86 -
Rwork0.243 1428 -
obs--94.86 %
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)
11.40480.06860.22860.75810.07122.2169-0.0412-0.05310.08070.03310.03920.1248-0.0861-0.43110.00190.11880.0645-0.0110.16750.00230.0527-25.3-1.99443.146
21.68740.11030.10781.1853-0.84274.56-0.0605-0.0824-0.07290.13020.043-0.0374-0.0624-0.04990.01750.0985-0.00640.01620.0692-0.01110.0867-13.733-5.00448.128
31.19040.2078-0.12870.4095-0.17332.019-0.0191-0.0345-0.1659-0.0108-0.0312-0.00260.1624-0.19250.05030.16490.0116-0.01120.1093-0.00630.0431-16.357-8.87744.15
42.08970.66620.16911.4828-0.02351.7733-0.09650.37670.3847-0.19850.07680.1411-0.311-0.20640.01970.17180.0532-0.02270.13480.07060.0714-9.079.97726.426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 196
2X-RAY DIFFRACTION2A197 - 238
3X-RAY DIFFRACTION3A239 - 352
4X-RAY DIFFRACTION4A353 - 466

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