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- PDB-3hbq: Structure of recombinant Chicken Liver Sulfite Oxidase mutant Cys... -

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Basic information

Entry
Database: PDB / ID: 3hbq
TitleStructure of recombinant Chicken Liver Sulfite Oxidase mutant Cys 185 Ala
ComponentsSulphite oxide
KeywordsOXIDOREDUCTASE / Molybdenum / molybdopterin / oxotransferase / metal binding / sulfite oxidase
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
HYDROXY(DIOXO)MOLYBDENUM / Chem-MTE / Sulfite oxidase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsQiu, J.A.
CitationJournal: Biochemistry / Year: 2010
Title: The structures of the C185S and C185A mutants of sulfite oxidase reveal rearrangement of the active site.
Authors: Qiu, J.A. / Wilson, H.L. / Pushie, M.J. / Kisker, C. / George, G.N. / Rajagopalan, K.V.
History
DepositionMay 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Sulphite oxide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6024
Polymers50,9691
Non-polymers6323
Water86548
1
A: Sulphite oxide
hetero molecules

A: Sulphite oxide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2038
Polymers101,9382
Non-polymers1,2656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545-x,-y-1,z1
Buried area5260 Å2
ΔGint-31 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.284, 86.284, 152.991
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 Sulphite oxide


Mass: 50969.125 Da / Num. of mol.: 1 / Fragment: rCSO C185A residues 94 to 466 / Mutation: Cys 185 Ala
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: sulfite oxidase / Plasmid: pTRC99a rCSO C185A / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 / References: UniProt: P07850*PLUS
#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-MOM / HYDROXY(DIOXO)MOLYBDENUM


Mass: 144.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HMoO3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% (w/v) PEG 4000 and 150 mM Ammonium sulfate, and 100 mM MES pH 6.0 , 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 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: 2.8→47.67 Å / Num. all: 13652 / Num. obs: 13652 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.068 / Net I/σ(I): 27.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 4.8 / Rsym value: 0.242 / % possible all: 94.3

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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: 2.8→47.67 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 22.505 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.819 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22791 676 5 %RANDOM
Rwork0.17513 ---
obs0.17768 12963 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å2-0 Å2
2--0.59 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2879 0 34 48 2961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223001
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9684110
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02922.348132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97615433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.011531
X-RAY DIFFRACTIONr_chiral_restr0.0940.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0222373
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6811.51867
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25323014
X-RAY DIFFRACTIONr_scbond_it1.94231134
X-RAY DIFFRACTIONr_scangle_it3.2354.51096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 48 -
Rwork0.279 865 -
obs--91.39 %
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)
11.9926-0.65640.26282.9057-1.11683.63550.0326-0.03690.18640.2846-0.0774-0.1565-0.95930.09840.04490.5153-0.1347-0.04040.3734-0.02450.031-2.77-14.929-31.661
21.7491-0.1737-0.42522.1312-0.31154.865-0.048-0.0821-0.0301-0.03660.0044-0.089-0.14470.28390.04360.256-0.0197-0.00710.2610.00150.0297-2.844-28.423-32.028
30.59040.4652-0.62.9184-0.69474.0866-0.1235-0.06520.0710.12580.07260.1237-0.4984-0.11050.0510.3518-0.0205-0.02370.41010.01060.0171-6.183-23.331-26.434
45.8452-0.19050.55375.33215.86236.5707-0.37770.3999-0.7199-0.6963-0.44830.9157-0.8137-0.46410.8260.23730.0097-0.11690.46360.00780.3059-18.1-32.64-40.583
53.4302-0.3125-1.29363.1655-0.08095.51560.05520.1760.0846-0.4564-0.1878-0.5419-0.2980.88780.13260.2935-0.07640.06160.49530.06870.097111.373-33.612-48.003
62.0369-0.660.58583.18960.72164.57830.00580.33540.213-0.5885-0.093-0.3113-0.35240.52550.08720.3328-0.04390.05050.49970.05320.04487.075-34.254-50.302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 173
2X-RAY DIFFRACTION2A174 - 236
3X-RAY DIFFRACTION3A237 - 310
4X-RAY DIFFRACTION4A311 - 341
5X-RAY DIFFRACTION5A342 - 401
6X-RAY DIFFRACTION6A402 - 466

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