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- PDB-1y67: Crystal Structure of Manganese Superoxide Dismutase from Deinococ... -

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Basic information

Entry
Database: PDB / ID: 1y67
TitleCrystal Structure of Manganese Superoxide Dismutase from Deinococcus radiodurans
ComponentsManganese Superoxide dismutase
KeywordsOXIDOREDUCTASE / SUPEROXIDE DISMUTASE / MANGANESE ENZYME / METALLOPROTEIN
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / removal of superoxide radicals / 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 [Mn]
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 Å
AuthorsChan, S. / Tanaka, S. / Sawaya, M.R. / Perry, L.J.
Citation
Journal: To be Published
Title: Crystal Structure of Manganese Superoxide Dismutase from Deinococcus radiodurans
Authors: Chan, S. / Tanaka, S. / Sawaya, M.R. / Perry, L.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Refinement of Macromolecular Structures by the Maximum-Likelihood Method
Authors: Murshudov, G.N.
History
DepositionDec 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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_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 / _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 / _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: Manganese Superoxide dismutase
B: Manganese Superoxide dismutase
C: Manganese Superoxide dismutase
D: Manganese Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1058
Polymers101,8814
Non-polymers2234
Water7,134396
1
A: Manganese Superoxide dismutase
B: Manganese Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0524
Polymers50,9412
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Manganese Superoxide dismutase
D: Manganese Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0524
Polymers50,9412
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.801, 87.922, 116.198
Angle α, β, γ (deg.)90.000, 91.140, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer formed from either chains A and B or chains C and D.

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Components

#1: Protein
Manganese Superoxide dismutase / MnSOD


Mass: 25470.299 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: sodA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: Q9RUV2, superoxide dismutase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.43 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 200mM ammonium acetate (pH 7.1) 20%(w/v) PEG3350, 0.3M NaCl, 0.3M imidazole, 20mM Tris (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→119.5 Å / Num. all: 74526 / Num. obs: 74526 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 31.7 Å2 / Rsym value: 0.074 / Net I/σ(I): 15.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 7437 / Rsym value: 0.493 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VEW

1vew


Resolution: 1.853→119.523 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.121 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3697 4.961 %RANDOM
Rwork0.1841 ---
all0.185 74526 --
obs0.185 74526 99.559 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.125 Å2
Baniso -1Baniso -2Baniso -3
1-1.903 Å20 Å2-1.797 Å2
2---0.959 Å20 Å2
3----1.016 Å2
Refine analyzeLuzzati coordinate error obs: 0.205 Å
Refinement stepCycle: LAST / Resolution: 1.853→119.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6565 0 4 396 6965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216743
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9189172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2125825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44324.83352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.946151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1971529
X-RAY DIFFRACTIONr_chiral_restr0.0840.2953
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025333
X-RAY DIFFRACTIONr_nbd_refined0.1860.22992
X-RAY DIFFRACTIONr_nbtor_refined0.2980.24663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2420
X-RAY DIFFRACTIONr_metal_ion_refined0.0250.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.217
X-RAY DIFFRACTIONr_mcbond_it0.541.54241
X-RAY DIFFRACTIONr_mcangle_it0.86226570
X-RAY DIFFRACTIONr_scbond_it1.44632933
X-RAY DIFFRACTIONr_scangle_it2.2794.52602
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.853-1.9010.2792660.2415071554996.179
1.901-1.9530.2422830.225039533199.831
1.953-2.0090.2352370.1995007524599.981
2.009-2.0710.2392600.1944804506599.98
2.071-2.1390.2262450.19146734918100
2.139-2.2140.2152270.1874524475299.979
2.214-2.2980.2022230.1854403462799.978
2.298-2.3910.2092290.19141824411100
2.391-2.4980.2352070.1914016422499.976
2.498-2.620.2192140.19438594073100
2.62-2.7610.221820.1993716390099.949
2.761-2.9290.2371740.1923475365199.945
2.929-3.1310.2021650.1923287345399.971
3.131-3.3810.1911530.1833053320799.969
3.381-3.7040.1881530.1722776293999.66
3.704-4.1410.1991320.1522528268199.217
4.141-4.780.1671150.1522240237199.325
4.78-5.8520.173920.181905200599.601
5.852-8.2660.192900.1951466156499.488
8.266-119.5230.147500.17680589096.067
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)
10.66030.34110.5032.47640.37811.5235-0.0502-0.0190.0351-0.31580.00770.0475-0.04910.06610.0424-0.1359-0.02490.0135-0.1242-0.0019-0.1349-9.949416.496214.235
21.4630.26521.11581.91440.17772.524-0.1047-0.08250.1760.1919-0.081-0.0461-0.29490.01070.1857-0.1419-0.0441-0.0023-0.1051-0.031-0.14910.30527.959439.7315
31.29650.32480.47722.03451.15122.37830.03550.2108-0.0167-0.16210.146-0.06710.00030.0197-0.1815-0.1447-0.0044-0.0157-0.0939-0.0078-0.16088.388826.493272.5899
41.20850.19240.56071.35540.35881.77430.17230.0062-0.19390.34590.0118-0.12970.3405-0.0201-0.18410.0373-0.0063-0.1017-0.20630.0129-0.117316.966118.79100.5325
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 932 - 94
21AA97 - 21398 - 214
32BB1 - 902 - 91
42BB98 - 21199 - 212
53CC2 - 893 - 90
63CC98 - 21399 - 214
74DD2 - 2153 - 216

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