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- PDB-3g50: Crystal Structure of NiSOD D3A mutant at 1.9 A -

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Basic information

Entry
Database: PDB / ID: 3g50
TitleCrystal Structure of NiSOD D3A mutant at 1.9 A
ComponentsSuperoxide dismutase [Ni]
KeywordsOXIDOREDUCTASE / Nickel / Hexamer / Superoxide dismutase / NiSOD / SOD / Antioxidant / Metal-binding
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / nickel cation binding / cytoplasm
Similarity search - Function
Nickel-containing superoxide dismutase / Superoxide dismutase, Nickel-type / Nickel-containing superoxide dismutase superfamily / Nickel-containing superoxide dismutase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / Superoxide dismutase [Ni]
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsGarman, S.C. / Guce, A.I. / Herbst, R.W. / Bryngelson, P.A. / Cabelli, D.E. / Higgins, K.A. / Ryan, K.C. / Maroney, M.J.
CitationJournal: Biochemistry / Year: 2009
Title: Role of conserved tyrosine residues in NiSOD catalysis: a case of convergent evolution
Authors: Herbst, R.W. / Guce, A. / Bryngelson, P.A. / Higgins, K.A. / Ryan, K.C. / Cabelli, D.E. / Garman, S.C. / Maroney, M.J.
History
DepositionFeb 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Ni]
B: Superoxide dismutase [Ni]
C: Superoxide dismutase [Ni]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6545
Polymers39,5373
Non-polymers1172
Water5,242291
1
A: Superoxide dismutase [Ni]
B: Superoxide dismutase [Ni]
C: Superoxide dismutase [Ni]
hetero molecules

A: Superoxide dismutase [Ni]
B: Superoxide dismutase [Ni]
C: Superoxide dismutase [Ni]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,30910
Polymers79,0746
Non-polymers2354
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area13630 Å2
ΔGint-62 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.988, 112.274, 111.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-153-

HOH

21C-121-

HOH

31C-182-

HOH

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Components

#1: Protein Superoxide dismutase [Ni] / NiSOD / Nickel-containing superoxide dismutase


Mass: 13178.955 Da / Num. of mol.: 3 / Fragment: NiSOD (UNP residues 15 to 131) / Mutation: D3A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: 2SC7G11.16c, SCO5254, sod1, sodN / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P80735, superoxide dismutase
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 550 MME, MgCl2, HEPES, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9184 Å
DetectorType: ADSC / Detector: CCD / Date: Aug 14, 2007
RadiationProtocol: SINGLE WAVELENGTH WITH ANOMALOUS / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→21.57 Å / Num. obs: 29881 / % possible obs: 99.9 % / Redundancy: 8 % / Rsym value: 0.046 / Net I/σ(I): 41.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.929 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→21.57 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.493 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23986 1519 5.1 %RANDOM
Rwork0.18579 ---
obs0.18854 28277 99.5 %-
all-29945 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.978 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 2 291 3046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222849
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9453858
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6525347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84624.701134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9211512
X-RAY DIFFRACTIONr_chiral_restr0.1160.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212166
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.21470
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21983
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.2118
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9771.51743
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71722807
X-RAY DIFFRACTIONr_scbond_it2.77831106
X-RAY DIFFRACTIONr_scangle_it4.5684.51049
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 108 -
Rwork0.292 1990 -
obs--96.24 %
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)
13.3065-2.2944-2.89641.59262.00682.57170.0459-0.15870.3548-0.00310.1477-0.2509-0.03860.1305-0.19360.08250.0492-0.02460.0574-0.00120.2727-13.939821.040128.9185
21.6644-0.5339-0.05060.85420.05370.31750.02010.04280.1308-0.07650.0088-0.0306-0.11920.0151-0.02890.0503-0.00580.0110.00510.00460.01431.043224.302216.2586
30.71312.64811.29769.85144.82752.36570.0949-0.03980.05990.4109-0.18760.21320.2028-0.08630.09270.0648-0.0255-0.01210.0590.00180.0515-16.9011-4.662928.5532
41.3180.7141-0.53920.8044-0.32430.9177-0.04030.1058-0.0337-0.08140.00850.04150.0856-0.02180.03180.02240.0046-0.00350.0147-0.00930.01071.0589-7.598916.3177
50.0017-0.0009-0.00270.00070.00220.0081-0.0187-0.00540.00870.01430.00880.00160.05330.01240.010.3560.06580.02680.19790.03260.2055-2.51297.710246.6597
60.637-0.1622-0.47750.60940.34971.38460.0071-0.06670.02250.08990.0034-0.10020.03460.0967-0.01050.0152-0.0045-0.01480.01960.00180.018615.9718.586639.9301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 116
3X-RAY DIFFRACTION3B4 - 7
4X-RAY DIFFRACTION4B8 - 116
5X-RAY DIFFRACTION5C1 - 7
6X-RAY DIFFRACTION6C8 - 116

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