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- PDB-1ej8: CRYSTAL STRUCTURE OF DOMAIN 2 OF THE YEAST COPPER CHAPERONE FOR S... -

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Basic information

Entry
Database: PDB / ID: 1ej8
TitleCRYSTAL STRUCTURE OF DOMAIN 2 OF THE YEAST COPPER CHAPERONE FOR SUPEROXIDE DISMUTASE (LYS7) AT 1.55 A RESOLUTION
ComponentsLYS7
KeywordsCHAPERONE / beta barrel / copper chaperone for SOD / domain 2
Function / homology
Function and homology information


superoxide dismutase complex / superoxide dismutase copper chaperone activity / Detoxification of Reactive Oxygen Species / copper ion transport / protein folding chaperone complex / removal of superoxide radicals / mitochondrial intermembrane space / mitochondrial inner membrane / copper ion binding / mitochondrion ...superoxide dismutase complex / superoxide dismutase copper chaperone activity / Detoxification of Reactive Oxygen Species / copper ion transport / protein folding chaperone complex / removal of superoxide radicals / mitochondrial intermembrane space / mitochondrial inner membrane / copper ion binding / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Superoxide dismutase, copper/zinc binding domain / Heavy metal-associated domain, HMA / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase 1 copper chaperone
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.55 Å
AuthorsHall, L.T. / Sanchez, R.J. / Holloway, S.P. / Zhu, H. / Stine, J.E. / Lyons, T.J. / Demeler, B. / Schirf, V. / Hansen, J.C. / Nersissian, A.M. ...Hall, L.T. / Sanchez, R.J. / Holloway, S.P. / Zhu, H. / Stine, J.E. / Lyons, T.J. / Demeler, B. / Schirf, V. / Hansen, J.C. / Nersissian, A.M. / Valentine, J.S. / Hart, P.J.
CitationJournal: Biochemistry / Year: 2000
Title: X-ray crystallographic and analytical ultracentrifugation analyses of truncated and full-length yeast copper chaperones for SOD (LYS7): a dimer-dimer model of LYS7-SOD association and copper delivery.
Authors: Hall, L.T. / Sanchez, R.J. / Holloway, S.P. / Zhu, H. / Stine, J.E. / Lyons, T.J. / Demeler, B. / Schirf, V. / Hansen, J.C. / Nersissian, A.M. / Valentine, J.S. / Hart, P.J.
History
DepositionMar 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_symmetry / _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: LYS7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5022
Polymers15,4621
Non-polymers401
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.154, 46.326, 73.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LYS7


Mass: 15462.370 Da / Num. of mol.: 1 / Fragment: DOMAIN 2
Source method: isolated from a genetically manipulated source
Details: COPPER CHAPERONE FOR YEAST SOD
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET3D / Production host: Escherichia coli (E. coli) / References: UniProt: P40202
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 1.89 Å3/Da / Density % sol: 34.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, CaCl2, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
21 mMEDTA1drop
30.5 mMdithiothreitol1drop
450 mg/mlprotein1drop
5100 mMHEPES1reservoir
628 %PEG4001reservoir
7200 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→90 Å / Num. all: 17662 / Num. obs: 17203 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.6
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.346 / Num. unique all: 1530 / % possible all: 88.7
Reflection
*PLUS
Num. measured all: 78174
Reflection shell
*PLUS
% possible obs: 88.7 %

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Processing

Software
NameClassification
SHARPphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.55→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1719 -random
all0.196 17564 --
obs-17195 97.9 %-
Refinement stepCycle: LAST / Resolution: 1.55→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 1 112 1194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d2.2
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 2.2

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