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- PDB-1b4l: 15 ATMOSPHERE OXYGEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPER... -

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Basic information

Entry
Database: PDB / ID: 1b4l
Title15 ATMOSPHERE OXYGEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE
ComponentsPROTEIN (CU/ZN SUPEROXIDE DISMUTASE)
KeywordsOXIDOREDUCTASE / SUPEROXIDE ACCEPTOR / COPPER / ZINC
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 / SYNCHROTRON / OTHER / Resolution: 1.8 Å
AuthorsHart, P.J. / Balbirnie, M.M. / Ogihara, N.L. / Nersissian, A.M. / Weiss, M.S. / Valentine, J.S. / Eisenberg, D.
Citation
Journal: Biochemistry / Year: 1999
Title: A structure-based mechanism for copper-zinc superoxide dismutase.
Authors: Hart, P.J. / Balbirnie, M.M. / Ogihara, N.L. / Nersissian, A.M. / Weiss, M.S. / Valentine, J.S. / Eisenberg, D.
#1: Journal: Biochemistry / Year: 1996
Title: Unusual Trigonal-Planar Copper Configuration Revealed in the Atomic Structure of Yeast Copper-Zinc Superoxide Dismutase
Authors: Ogihara, N.L. / Parge, H.E. / Hart, P.J. / Weiss, M.S. / Goto, J. / Crane, B.R. / Tsang, J. / Slater, K. / Roe, J.A. / Valentine, J.S. / Eisenberg, D. / Tainer, J.A.
History
DepositionDec 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CU/ZN SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8723
Polymers15,7431
Non-polymers1292
Water2,090116
1
A: PROTEIN (CU/ZN SUPEROXIDE DISMUTASE)
hetero molecules

A: PROTEIN (CU/ZN SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7456
Polymers31,4872
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)118.900, 118.900, 75.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein PROTEIN (CU/ZN SUPEROXIDE DISMUTASE) / YEAST CU/ZN SOD


Mass: 15743.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CARLBIOTECH, COPENHAGEN / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / References: UniProt: P00445, superoxide dismutase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.25 Å3/Da / Density % sol: 61.7 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-25 mg/mlprotein11
250 mMphosphate11
32.0-2.2 Mammonium sulfate12
450 mMTris-HCl12
550 mM12NaCl
60.001 %(w/v)12NaN3

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 16745 / % possible obs: 87.7 % / Observed criterion σ(I): 0 / Redundancy: 3.88 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.048 / Net I/σ(I): 22
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 7.4 / Rsym value: 0.148 / % possible all: 90.5
Reflection
*PLUS
Num. measured all: 64930 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 90.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.8→10 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1671 10 %RANDOM
Rwork0.2 ---
obs0.2 16658 88.2 %-
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 2 116 1224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.279 --
Rwork0.264 1948 -
obs--93.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.279 / Rfactor Rwork: 0.264

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