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- PDB-5k3x: Crystal Structure of the sulfite dehydrogenase, SorT R78K mutant ... -

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Basic information

Entry
Database: PDB / ID: 5k3x
TitleCrystal Structure of the sulfite dehydrogenase, SorT R78K mutant from Sinorhizobium meliloti
ComponentsPutative sulfite oxidase
KeywordsOXIDOREDUCTASE / sulfite dehydrogenase / electron transfer / SUOX-fold
Function / homology
Function and homology information


sulfite oxidase / sulfite oxidase activity / sulfur compound metabolic process / molybdenum ion binding / molybdopterin cofactor binding / heme binding
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 / Twin arginine translocation (Tat) signal profile. ...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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Immunoglobulin E-set / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV) / Sulfite oxidase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLee, M. / McGrath, A. / Maher, M.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: The central active site arginine in sulfite oxidizing enzymes alters kinetic properties by controlling electron transfer and redox interactions.
Authors: Hsiao, J.C. / McGrath, A.P. / Kielmann, L. / Kalimuthu, P. / Darain, F. / Bernhardt, P.V. / Harmer, J. / Lee, M. / Meyers, K. / Maher, M.J. / Kappler, U.
History
DepositionMay 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Aug 12, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _struct_asym.entity_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative sulfite oxidase
B: Putative sulfite oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3707
Polymers79,0492
Non-polymers1,3215
Water14,610811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-28 kcal/mol
Surface area26550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.470, 95.720, 109.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative sulfite oxidase


Mass: 39524.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (bacteria) / Strain: 1021 / Gene: SMc04049 / Plasmid: pProex Htb / Production host: Escherichia coli (E. coli) / Strain (production host): TP1000 / References: UniProt: Q92M24, sulfite oxidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MTV / (MOLYBDOPTERIN-S,S)-DIOXO-THIO-MOLYBDENUM(IV)


Mass: 522.283 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13MoN5O8PS2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 811 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M PCB buffer pH 7, 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→72.1 Å / Num. obs: 102224 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.057 / Mean I/σ(I) obs: 1.6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PW9

4pw9


Resolution: 1.6→72.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.735 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17962 5110 5 %RANDOM
Rwork0.1552 ---
obs0.15644 97033 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.477 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.6→72.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5147 0 70 813 6030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195551
X-RAY DIFFRACTIONr_bond_other_d0.0020.025319
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9737613
X-RAY DIFFRACTIONr_angle_other_deg0.92312310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9525754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05224.703219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.29715914
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9661531
X-RAY DIFFRACTIONr_chiral_restr0.0870.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216367
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021190
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_it0.9761.5462823
X-RAY DIFFRACTIONr_mcbond_other0.9731.5452822
X-RAY DIFFRACTIONr_mcangle_it1.5782.3133544
X-RAY DIFFRACTIONr_mcangle_other1.5792.3143545
X-RAY DIFFRACTIONr_scbond_it1.6561.7272728
X-RAY DIFFRACTIONr_scbond_other1.6561.7272728
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6572.514036
X-RAY DIFFRACTIONr_long_range_B_refined5.69214.1176870
X-RAY DIFFRACTIONr_long_range_B_other4.93612.8676368
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 358 -
Rwork0.268 7060 -
obs--99.29 %

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