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- PDB-3sdp: THE 2.1 ANGSTROMS RESOLUTION STRUCTURE OF IRON SUPEROXIDE DISMUTA... -

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Basic information

Entry
Database: PDB / ID: 3sdp
TitleTHE 2.1 ANGSTROMS RESOLUTION STRUCTURE OF IRON SUPEROXIDE DISMUTASE FROM PSEUDOMONAS OVALIS
ComponentsIRON SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE (SUPEROXIDE ACCEPTOR)
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
: / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsStoddard, B.L. / Ringe, D. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 1990
Title: The 2.1-A resolution structure of iron superoxide dismutase from Pseudomonas ovalis.
Authors: Stoddard, B.L. / Howell, P.L. / Ringe, D. / Petsko, G.A.
#1: Journal: Protein Eng. / Year: 1990
Title: The Structure of Iron Superoxide Dismutase from Pseudomonas Ovalis Bound to the Inhibitor Azide: Coordination Changes and Dynamics During Catalysis
Authors: Stoddard, B.L. / Ringe, D. / Petsko, G.A.
History
DepositionMay 6, 1991Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IRON SUPEROXIDE DISMUTASE
B: IRON SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2144
Polymers43,1022
Non-polymers1122
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-25 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.900, 49.100, 61.700
Angle α, β, γ (deg.)90.00, 106.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein IRON SUPEROXIDE DISMUTASE


Mass: 21550.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / References: UniProt: P09223, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 85 OF EACH CHAIN IS IDENTIFIED AS ALA IN THIS ENTRY. NOTE THAT THIS RESIDUE IS IDENTIFIED ...RESIDUE 85 OF EACH CHAIN IS IDENTIFIED AS ALA IN THIS ENTRY. NOTE THAT THIS RESIDUE IS IDENTIFIED AS GLY IN SWISSPROT ENTRY SODF_PSEOV.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.8 / Method: batch method
Components of the solutions
*PLUS
Conc.: 55 %sat / Common name: ammonium sulfate

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 21140 / % possible obs: 72 % / Rmerge(I) obs: 0.086

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor obs: 0.232 / Highest resolution: 2.1 Å
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2910 0 2 180 3092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.033
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_plane_restr0.0220.025
X-RAY DIFFRACTIONp_chiral_restr0.2310.2

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