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- PDB-1sdy: STRUCTURE SOLUTION AND MOLECULAR DYNAMICS REFINEMENT OF THE YEAST... -

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Basic information

Entry
Database: PDB / ID: 1sdy
TitleSTRUCTURE SOLUTION AND MOLECULAR DYNAMICS REFINEMENT OF THE YEAST CU,ZN ENZYME SUPEROXIDE DISMUTASE
ComponentsCOPPER,ZINC SUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE(SUPEROXIDE ACCEPTOR)
Function / homology
Function and homology information


oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor / superoxide dismutase complex / negative regulation of cellular respiration / fungal-type cell wall organization / Platelet degranulation / Detoxification of Reactive Oxygen Species / copper ion transport / intracellular zinc ion homeostasis / cellular detoxification / superoxide metabolic process ...oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor / superoxide dismutase complex / negative regulation of cellular respiration / fungal-type cell wall organization / Platelet degranulation / Detoxification of Reactive Oxygen Species / copper ion transport / intracellular zinc ion homeostasis / cellular detoxification / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / intracellular copper ion homeostasis / removal of superoxide radicals / mitochondrial intermembrane space / cellular response to oxidative stress / protein stabilization / copper ion binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytosol
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsDjinovic, K. / Gatti, G. / Coda, A. / Antolini, L. / Pelosi, G. / Desideri, A. / Falconi, M. / Marmocchi, F. / Rotilio, G. / Bolognesi, M.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Structure solution and molecular dynamics refinement of the yeast Cu,Zn enzyme superoxide dismutase.
Authors: Djinovic, K. / Gatti, G. / Coda, A. / Antolini, L. / Pelosi, G. / Desideri, A. / Falconi, M. / Marmocchi, F. / Rolilio, G. / Bolognesi, M.
#1: Journal: Proteins / Year: 1989
Title: Evolution of Cuzn Superoxide Dismutase and the Greek Key Beta-Barrel Structural Motif
Authors: Getzoff, E.D. / Tainer, J.A. / Stempien, M.M. / Bell, G.I. / Hallewell, R.A.
#2: Journal: FEBS Lett. / Year: 1989
Title: Conservation of Local Electric Fields in the Evolution of Cu,Zn Superoxide Dismutase
Authors: Desideri, A. / Falconi, M. / Parisi, V. / Rotilio, G.
#3: Journal: Biochem.Biophys.Res.Commun. / Year: 1989
Title: Crystallographic Characterization and Three-Dimensional Model of Yeast Cu,Zn Superoxide Dismutase
Authors: Frigerio, F. / Falconi, M. / Gatti, G. / Bolognesi, M. / Desideri, A. / Marmocchi, F. / Rotilio, G.
History
DepositionJun 14, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX THE HELIX EXTENDS TO RESIDUE 129 AND TO RESIDUES 136, 137 AND 138 WITH BETA-TURNS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COPPER,ZINC SUPEROXIDE DISMUTASE
B: COPPER,ZINC SUPEROXIDE DISMUTASE
C: COPPER,ZINC SUPEROXIDE DISMUTASE
D: COPPER,ZINC SUPEROXIDE DISMUTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,48912
Polymers62,9744
Non-polymers5168
Water9,242513
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.300, 143.000, 62.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.60898, -0.79315, 0.00805), (-0.79175, 0.60845, 0.05401), (-0.04774, 0.02652, -0.99851)66.12, 32.642, 1.618
2given(-0.98276, 0.17205, -0.06771), (0.14718, 0.50631, -0.8497), (-0.11191, -0.84502, -0.5229)12.743, 31.966, 59.014
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN APPLIED TO CHAIN *D*.

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Components

#1: Protein
COPPER,ZINC SUPEROXIDE DISMUTASE


Mass: 15743.389 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00445, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / 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

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal grow
*PLUS
Temperature: 301 K / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.025 Mcitrate1drop
36 %(w/v)PEG40001drop
412 %(w/v)PEG40001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. obs: 32538 / % possible obs: 98.2 % / Num. measured all: 131852 / Rmerge(I) obs: 0.06

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.5→10 Å / Rfactor obs: 0.158
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4424 0 8 513 4945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.016
X-RAY DIFFRACTIONt_angle_deg2.912
X-RAY DIFFRACTIONt_dihedral_angle_d27.16
X-RAY DIFFRACTIONt_trig_c_planes0.019
X-RAY DIFFRACTIONt_gen_planes0.02
X-RAY DIFFRACTIONt_nbd0.098
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_planar_d0.019
X-RAY DIFFRACTIONt_plane_restr0.02

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