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- PDB-3g4x: Crystal Structure of NiSOD Y9F mutant -

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Basic information

Entry
Database: PDB / ID: 3g4x
TitleCrystal Structure of NiSOD Y9F mutant
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 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 / 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_ins_code / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)39,9039
Polymers39,6213
Non-polymers2826
Water7,008389
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)79,80718
Polymers79,2426
Non-polymers56512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area14260 Å2
ΔGint-61 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.089, 112.568, 111.866
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
11C-208-

HOH

21C-299-

HOH

31C-347-

HOH

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Components

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


Mass: 13206.965 Da / Num. of mol.: 3 / Fragment: NiSOD (UNP residues 15 to 131) / Mutation: Y9F
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.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 550 MME, CaCl2, Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 5, 2006
RadiationMonochromator: osmic blue / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 25440 / % possible obs: 99.4 % / Redundancy: 4.7 % / Rsym value: 0.054 / Net I/σ(I): 28
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.515 / % possible all: 98.3

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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
Starting model: PDB ENTRY 1T6U

1t6u


Resolution: 2.01→20.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.43 / SU B: 9.132 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23698 1300 5.1 %RANDOM
Rwork0.16817 ---
obs0.17169 24113 99.36 %-
all-25577 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.785 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.01→20.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 6 389 3182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222898
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.943926
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7595352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5624.892139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88115504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2971510
X-RAY DIFFRACTIONr_chiral_restr0.1090.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212225
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.21467
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21964
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2316
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.2135
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8271.51773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42322858
X-RAY DIFFRACTIONr_scbond_it2.56831125
X-RAY DIFFRACTIONr_scangle_it3.9684.51068
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.011→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 86 -
Rwork0.262 1709 -
obs--97.77 %
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)
14.6648-2.3041-4.00331.13831.97663.4384-0.1103-0.0517-0.02490.07070.05230.01080.10390.04070.0580.11430.0260.03530.06990.0130.1712-14.018320.925828.6046
21.4796-0.33050.01480.67420.03740.26420.0189-0.00160.059-0.11590.0227-0.0252-0.09640.0086-0.04160.0766-0.00420.04020.03280.0150.03691.012824.399616.2163
32.56491.043-0.62548.55714.4212.8403-0.20130.53710.65440.2851-0.03350.90390.2754-0.28940.23480.0748-0.0453-0.00630.14110.11220.2415-13.8784-3.916427.8616
41.37531.0482-0.92761.0003-0.49731.2129-0.08110.09360.0239-0.08890.0520.0430.1206-0.04680.02910.07410.00240.01680.0564-0.00140.01110.8616-8.030816.3168
55.7206-0.03681.10180.0018-0.07613.5409-0.2478-0.23140.0534-0.00460.0347-0.00620.1497-0.03860.21320.08960.00820.05320.0477-0.02130.0882-2.12337.984246.3197
60.4625-0.2078-0.56340.82290.35191.324-0.0061-0.0210.03230.11490.0074-0.12790.03110.0789-0.00130.0211-0.0024-0.02680.0589-0.00850.058316.17858.519539.8301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 116
3X-RAY DIFFRACTION3B1 - 7
4X-RAY DIFFRACTION4B8 - 116
5X-RAY DIFFRACTION5C1 - 7
6X-RAY DIFFRACTION6C8 - 116

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