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- PDB-6gsc: Sphingobacterium sp. T2 manganese superoxide dismutase catalyses ... -

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Basic information

Entry
Database: PDB / ID: 6gsc
TitleSphingobacterium sp. T2 manganese superoxide dismutase catalyses the oxidative demethylation of polymeric lignin via generation of hydroxyl radical
Components(Superoxide dismutase) x 2
KeywordsOXIDOREDUCTASE / LIGNIN VALORISATION / LIGNIN OXIDATION / MANGANESE KEYWDS 2 SUPEROXIDE DISMUTASE / SPHINGOBACTERIUM
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesSphingobacterium spiritivorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.32 Å
AuthorsRashid, G.M.M. / Zhang, X. / Wilkinson, R.C. / Fulop, V. / Cottyn, B. / Baumberger, S. / Bugg, T.D.H.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M025772/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M003523/1 United Kingdom
European Commission720303
Citation
Journal: ACS Chem. Biol. / Year: 2018
Title: Sphingobacterium sp. T2 Manganese Superoxide Dismutase Catalyzes the Oxidative Demethylation of Polymeric Lignin via Generation of Hydroxyl Radical.
Authors: Rashid, G.M.M. / Zhang, X. / Wilkinson, R.C. / Fulop, V. / Cottyn, B. / Baumberger, S. / Bugg, T.D.H.
#1: Journal: ACS Chem. Biol. / Year: 2015
Title: Identification of Manganese Superoxide Dismutase from Sphingobacterium sp. T2 as a Novel Bacterial Enzyme for Lignin Oxidation.
Authors: Rashid, G.M. / Taylor, C.R. / Liu, Y. / Zhang, X. / Rea, D. / Fulop, V. / Bugg, T.D.
History
DepositionJun 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.3Jan 17, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0564
Polymers45,9462
Non-polymers1102
Water10,593588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-12 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.530, 58.610, 75.070
Angle α, β, γ (deg.)90.00, 90.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Superoxide dismutase


Mass: 22908.562 Da / Num. of mol.: 1 / Mutation: A31H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobacterium spiritivorum (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3KL50, superoxide dismutase
#2: Protein Superoxide dismutase


Mass: 23037.744 Da / Num. of mol.: 1 / Mutation: A31H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobacterium spiritivorum (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3KL50, superoxide dismutase
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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 Å3/Da / Density % sol: 37 % / Description: rod shape
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 130 mM ammonium citrate, 26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2018 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.32→40 Å / Num. obs: 94757 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Rrim(I) all: 0.093 / Net I/σ(I): 14.3
Reflection shellResolution: 1.32→1.39 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 2 / Num. unique obs: 6973 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5a9g

5a9g


Resolution: 1.32→39.66 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.756 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.046 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16632 3769 4 %RANDOM
Rwork0.15031 ---
obs0.15094 90988 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.911 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0 Å2-0.44 Å2
2--0.5 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.32→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3249 0 2 588 3839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193335
X-RAY DIFFRACTIONr_bond_other_d0.0010.023091
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9334535
X-RAY DIFFRACTIONr_angle_other_deg0.83937123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11925.063158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45115540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3071510
X-RAY DIFFRACTIONr_chiral_restr0.1120.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02779
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 275 -
Rwork0.243 6696 -
obs--99.94 %

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