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- PDB-3g4z: Crystal Structure of NiSOD Y9F mutant at 1.9 A -

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Basic information

Entry
Database: PDB / ID: 3g4z
TitleCrystal Structure of NiSOD Y9F 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
BROMIDE ION / NICKEL (II) ION / Superoxide dismutase [Ni]
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 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 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Oct 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_seq_id
Revision 1.5Feb 21, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)40,0379
Polymers39,6213
Non-polymers4166
Water8,251458
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)80,07318
Polymers79,2426
Non-polymers83212
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area14200 Å2
ΔGint-63 kcal/mol
Surface area26280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.876, 111.577, 111.553
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-187-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 3 - 116 / Label seq-ID: 3 - 116

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CC

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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 / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 293 K / pH: 6.5
Details: PEG 550 MME, Bis-Tris, 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
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: 1.87→20.9 Å / Num. obs: 29628 / % possible obs: 95.3 % / Redundancy: 7.1 % / Rsym value: 0.03 / Net I/σ(I): 42.1
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.337 / % possible all: 91

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→20.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.647 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1452 5 %RANDOM
Rwork0.183 ---
obs0.186 27302 92.6 %-
all-31050 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.87→20.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 6 458 3255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222873
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9433888
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.045348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23924.891137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66315501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.751511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212192
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.21554
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21994
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3150.2149
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.272
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.51763
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55222837
X-RAY DIFFRACTIONr_scbond_it2.53631110
X-RAY DIFFRACTIONr_scangle_it4.1794.51051
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 906 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.280.5
2Cmedium thermal1.092
LS refinement shellResolution: 1.87→1.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 93 -
Rwork0.309 1835 -
obs--84.82 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / Refine-ID: X-RAY DIFFRACTION

ID
1
2
3
4
5
6
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 10
2X-RAY DIFFRACTION2A11 - 117
3X-RAY DIFFRACTION3B1 - 10
4X-RAY DIFFRACTION4B11 - 117
5X-RAY DIFFRACTION5C1 - 10
6X-RAY DIFFRACTION6C11 - 117

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