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- PDB-2b7j: Crystal Structure of Yeast Sco1 with Copper Bound -

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Basic information

Entry
Database: PDB / ID: 2b7j
TitleCrystal Structure of Yeast Sco1 with Copper Bound
ComponentsSCO1 protein
KeywordsMETAL BINDING PROTEIN / Metallochaperone / Cytochrome c Oxidase / Sco / Sco1
Function / homology
Function and homology information


copper chaperone activity / mitochondrial cytochrome c oxidase assembly / intracellular copper ion homeostasis / cell redox homeostasis / cellular response to oxidative stress / mitochondrial inner membrane / copper ion binding / mitochondrion
Similarity search - Function
Synthesis of cytochrome c oxidase, Sco1/Sco2 / Copper chaperone SCO1/SenC / SCO1/SenC / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Protein SCO1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAbajian, C. / Rosenzweig, A.C.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2006
Title: Crystal structure of yeast Sco1.
Authors: Abajian, C. / Rosenzweig, A.C.
History
DepositionOct 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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
Revision 1.4Oct 30, 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: SCO1 protein
B: SCO1 protein
C: SCO1 protein
D: SCO1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,00510
Polymers91,6244
Non-polymers3816
Water2,414134
1
A: SCO1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0974
Polymers22,9061
Non-polymers1913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SCO1 protein


Theoretical massNumber of molelcules
Total (without water)22,9061
Polymers22,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SCO1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0974
Polymers22,9061
Non-polymers1913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SCO1 protein


Theoretical massNumber of molelcules
Total (without water)22,9061
Polymers22,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.600, 81.900, 79.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
SCO1 protein


Mass: 22905.924 Da / Num. of mol.: 4 / Fragment: residues 96-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCO1 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P23833
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 291 K / pH: 5.3
Details: Lithium Sulfate, Sodium Citrate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 5.30

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.3768
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 27, 2005
RadiationMonochromator: GLASS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3768 Å / Relative weight: 1
ReflectionResolution: 2.3→81.65 Å / Num. obs: 24962 / % possible obs: 79 % / Observed criterion σ(I): 0 / Rsym value: 0.062 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.42 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.3 / % possible all: 42.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B7K

2b7k


Resolution: 2.3→81.65 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.252 2481 RANDOM
Rwork0.21 --
obs0.21 24948 -
all-24948 -
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1-8.533 Å20 Å20 Å2
2---14.331 Å20 Å2
3---5.798 Å2
Refinement stepCycle: LAST / Resolution: 2.3→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 6 134 5580
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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