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- PDB-5a9g: Manganese Superoxide Dismutase from Sphingobacterium sp. T2 -

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Basic information

Entry
Database: PDB / ID: 5a9g
TitleManganese Superoxide Dismutase from Sphingobacterium sp. T2
ComponentsMANGANESE SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / LIGNIN VALORISATION / LIGNIN OXIDATION / MANGANESE 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 / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRashid, G.M.M. / Taylor, C.R. / Liu, Y. / Zhang, X. / Rea, D. / Fulop, V. / Bugg, T.D.H.
CitationJournal: 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.H.
History
DepositionJul 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _struct_conn.ptnr2_label_seq_id / _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: MANGANESE SUPEROXIDE DISMUTASE
B: MANGANESE SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9694
Polymers52,8592
Non-polymers1102
Water10,827601
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-12.1 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.700, 58.940, 75.710
Angle α, β, γ (deg.)90.00, 90.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MANGANESE SUPEROXIDE DISMUTASE


Mass: 26429.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPHINGOBACTERIUM SPIRITIVORUM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL50*PLUS, superoxide dismutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 601 / 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: NONE
Crystal growpH: 8.5
Details: 20% (W/V) PEG 3350, 0.2 M DI-AMMONIUM HYDROGEN CITRATE, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2014 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.35→37 Å / Num. obs: 87001 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.2
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.5 / % possible all: 79

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RCV

2rcv


Resolution: 1.35→36.6 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.307 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.15663 3412 3.9 %RANDOM
Rwork0.13761 ---
obs0.13838 83589 96.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.463 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20.29 Å2
2--0.06 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.35→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 2 601 3851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193332
X-RAY DIFFRACTIONr_bond_other_d0.0010.023098
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9364530
X-RAY DIFFRACTIONr_angle_other_deg0.95837140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62525.128156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51415542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2131510
X-RAY DIFFRACTIONr_chiral_restr0.1610.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02772
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: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 165 -
Rwork0.286 4530 -
obs--71.32 %
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)
10.3637-0.0383-0.11650.1150.10410.16170.0186-0.00010.0315-0.0093-0.0146-0.0192-0.02520.018-0.0040.0313-0.002-0.00790.0283-0.0010.041433.354950.805910.8371
20.5168-0.18870.08110.287-0.14560.07540.00980.0422-0.012-0.00890.0060.03130.0083-0.0005-0.01590.03370.0042-0.01680.0310.00270.033415.325645.42677.0422
30.32410.03220.07280.0211-0.03970.140.01920.01230.01860.0047-0.00380.00990.00070.0139-0.01550.04090.003-0.00910.025-0.00410.029719.839648.489113.5646
40.46030.12990.15390.23970.17290.29050.0046-0.0312-0.0596-0.0048-0.01280.0372-0.01710.02490.00820.0249-0.003-0.01660.03890.00970.034422.684623.104129.2923
50.7401-0.14110.07380.2497-0.1220.0788-0.00910.0094-0.067-0.0211-0.0149-0.0221-0.00790.02380.0240.0268-0.0004-0.01290.04410.01160.042140.628121.48622.8645
60.25690.0855-0.12580.0612-0.03020.06640.0151-0.0565-0.0305-0.0159-0.0286-0.0212-0.01690.02840.01350.0337-0.0019-0.01930.04770.01630.038436.187226.321928.2666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 90
2X-RAY DIFFRACTION2A91 - 150
3X-RAY DIFFRACTION3A151 - 202
4X-RAY DIFFRACTION4B-3 - 90
5X-RAY DIFFRACTION5B91 - 150
6X-RAY DIFFRACTION6B151 - 202

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