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- PDB-1wb8: Iron Superoxide Dismutase (FE-SOD) from the Hyperthermophile SULF... -

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Basic information

Entry
Database: PDB / ID: 1wb8
TitleIron Superoxide Dismutase (FE-SOD) from the Hyperthermophile SULFOLOBUS SOLFATARICUS. 2.3 A Resolution Structure of Recombinant Protein with a Covalently Modified Tyrosine in the Active Site.
ComponentsSUPEROXIDE DISMUTASE [FE]
KeywordsOXIDOREDUCTASE / SUPEROXIDE DISMUTASE / SOD / IRON / SUPEROXIDE RADICAL DISPROPORTIONATION / SULFOLOBUS SOLFTARICUS / THERMOSTABLE
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / 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 ...: / 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
: / phenylmethanesulfonic acid / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUrsby, T. / Adinolfi, B.S. / Al-Karadaghi, S. / De Vendittis, E. / Bocchini, V.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Iron Superoxide Dismutase from the Archaeon Sulfolobus Solfataricus: Analysis of Structure and Thermostability
Authors: Ursby, T. / Adinolfi, B.S. / Al-Karadaghi, S. / De Vendittis, E. / Bocchini, V.
#1: Journal: Eur.J.Biochem. / Year: 2001
Title: Phenylmethanesulfonyl Fluoride Inactivates an Archaeal Superoxide Dismutase by Chemical Modification of a Specific Tyrosine Residue
Authors: De Vendittis, E. / Ursby, T. / Rullo, R. / Gogliettino, M.A. / Masullo, M. / Bocchini, V.
History
DepositionOct 31, 2004Deposition site: PDBE / Processing site: PDBE
SupersessionNov 8, 2004ID: 1SSS
Revision 1.0Nov 8, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE [FE]
B: SUPEROXIDE DISMUTASE [FE]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7416
Polymers48,2852
Non-polymers4564
Water3,117173
1
A: SUPEROXIDE DISMUTASE [FE]
B: SUPEROXIDE DISMUTASE [FE]
hetero molecules

A: SUPEROXIDE DISMUTASE [FE]
B: SUPEROXIDE DISMUTASE [FE]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,48112
Polymers96,5694
Non-polymers9128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)76.266, 124.324, 60.268
Angle α, β, γ (deg.)90.00, 128.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2069-

HOH

21B-2058-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.90666, -0.00174, 0.42185), (-0.00168, -1, -0.00052), (0.42185, -0.00023, -0.90666)
Vector: -11.57396, 96.02196, 52.78307)

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Components

#1: Protein SUPEROXIDE DISMUTASE [FE]


Mass: 24142.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENT MODIFICATION OF TYR 41 CONSISTING OF HET GROUP PMS (PHENYL METHYL SULFONATE, BENZYLSULFINIC ACID)
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PT7-7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P80857, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: CRYSTALS WERE GROWN BY VAPOR DIFFUSION IN HANGING DROPS AT 21C IN A 1 TO 1 MIX OF THE RESERVOIR SOLUTION (8% PEG 8000, 0.1 M TRIS/HCL PH 8.5) AND A PROTEIN SOLUTION (2.0 MG/ML SSSOD).

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ROTAFLEX RU-2 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 9, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→62 Å / Num. obs: 18647 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3 / % possible all: 94.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ABM

1abm
PDB Unreleased entry


Resolution: 2.3→22.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3370580.24 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
Details: NOTE THAT RESIDUES 1-3 AND 209- -210 OF THE COMPLETE SEQUENCE ARE MISSING IN THIS ENTRY DUE TO DISORDER IN THE CRYSTAL. THE NCS USED IN THE REFINEMENT INCLUDED MOLECULE A EXCEPT 19 RESIDUES, ...Details: NOTE THAT RESIDUES 1-3 AND 209- -210 OF THE COMPLETE SEQUENCE ARE MISSING IN THIS ENTRY DUE TO DISORDER IN THE CRYSTAL. THE NCS USED IN THE REFINEMENT INCLUDED MOLECULE A EXCEPT 19 RESIDUES, THE IRON ION AND 68 WATER MOLECULES AND THE CORRESPONDING NCS RELEATED ATOMS. THE RMS DEVIATION FOR THE ATOMS USED FOR NCS IN THE REFINEMENT IS 0.006 A.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 955 5.1 %RANDOM
Rwork0.167 ---
obs0.167 18643 95.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.1856 Å2 / ksol: 0.294185 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å20 Å2-0.41 Å2
2--4.85 Å20 Å2
3----1.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→22.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 22 173 3537
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.350.5
X-RAY DIFFRACTIONc_mcangle_it0.641
X-RAY DIFFRACTIONc_scbond_it2.783
X-RAY DIFFRACTIONc_scangle_it3.913.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 157 5.2 %
Rwork0.208 2834 -
obs--92.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PMS.PARPMS.TOP

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