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- PDB-3ljf: The X-ray structure of iron superoxide dismutase from Pseudoalter... -

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Basic information

Entry
Database: PDB / ID: 3ljf
TitleThe X-ray structure of iron superoxide dismutase from Pseudoalteromonas haloplanktis (crystal form II)
Componentsiron superoxide dismutase
KeywordsOXIDOREDUCTASE / cold adaptation / superoxide dismutase / flexibility / thermal stability / psychrophilic protein / Metal-binding
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
trehalose / : / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesPseudoalteromonas haloplanktis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMerlino, A. / Russo Krauss, I. / Rossi, B. / Conte, M. / Vergara, A. / Sica, F.
Citation
Journal: J.Struct.Biol. / Year: 2010
Title: Structure and flexibility in cold-adapted iron superoxide dismutases: the case of the enzyme isolated from Pseudoalteromonas haloplanktis.
Authors: Merlino, A. / Russo Krauss, I. / Castellano, I. / De Vendittis, E. / Rossi, B. / Conte, M. / Vergara, A. / Sica, F.
#1: Journal: Protein and Peptide letters / Year: 2008
Title: Crystallization and preliminary x-ray diffraction studies of a psychrophilic iron superoxide dismutase from Pseudoalteromonas haloplanktis
Authors: Merlino, A. / Russo Krauss, I. / Castellano, I. / De Vendittis, E. / Vergara, A. / Sica, F.
History
DepositionJan 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: iron superoxide dismutase
C: iron superoxide dismutase
B: iron superoxide dismutase
D: iron superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,67112
Polymers85,0784
Non-polymers1,5938
Water9,584532
1
A: iron superoxide dismutase
B: iron superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3356
Polymers42,5392
Non-polymers7964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-8 kcal/mol
Surface area15900 Å2
MethodPISA
2
C: iron superoxide dismutase
D: iron superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3356
Polymers42,5392
Non-polymers7964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-8 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.476, 103.785, 90.251
Angle α, β, γ (deg.)90.00, 103.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
iron superoxide dismutase


Mass: 21269.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria)
Strain: TAC 125 / Gene: sodB, PSHAa1215 / Production host: Escherichia coli (E. coli) / References: UniProt: P84612, superoxide dismutase
#2: Polysaccharide
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: Crystals of protein were obtained using 2.3-2.5M ammonium sulphate, 10 mM FeCl3, 100 mM HEPES pH 7.0, 3% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 26, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 51958 / Num. obs: 51958 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.092

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ISA

1isa


Resolution: 2.1→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 4727 random
Rwork0.192 --
all0.215 42414 -
obs0.192 47141 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 96 532 6672

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