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- PDB-2ggt: Crystal structure of human SCO1 complexed with nickel. -

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Basic information

Entry
Database: PDB / ID: 2ggt
TitleCrystal structure of human SCO1 complexed with nickel.
ComponentsSCO1 protein homolog, mitochondrial
KeywordsCHAPERONE / Copper chaperone / Cu-binding protein / mitochondrial assembly factor / redox / Nickel / Disuplhide / Mitochondrion
Function / homology
Function and homology information


Complex IV assembly / copper chaperone activity / mitochondrial cytochrome c oxidase assembly / myofibril / intracellular copper ion homeostasis / 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
NICKEL (II) ION / Protein SCO1 homolog, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBanci, L. / Bertini, I. / Calderone, V. / Ciofi-Baffoni, S. / Mangani, S. / Martinelli, M. / Palumaa, P. / Wang, S.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: A hint for the function of human Sco1 from different structures.
Authors: Banci, L. / Bertini, I. / Calderone, V. / Ciofi-Baffoni, S. / Mangani, S. / Martinelli, M. / Palumaa, P. / Wang, S.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of human SCO1: implications for redox signaling by a mitochondrial cytochrome c oxidase 'assembly' protein.
Authors: Williams, J.C. / Sue, C. / Banting, G.S. / Yang, H. / Glerum, D.M. / Hendrickson, W.A. / Schon, E.A.
#2: Journal: Structure / Year: 2003
Title: Solution structure of Sco1: a thioredoxin-like protein Involved in cytochrome c oxidase assembly.
Authors: Balatri, E. / Banci, L. / Bertini, I. / Cantini, F. / Ciofi-Baffoni, S.
History
DepositionMar 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SCO1 protein homolog, mitochondrial
B: SCO1 protein homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6856
Polymers37,4962
Non-polymers1884
Water1,02757
1
A: SCO1 protein homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8423
Polymers18,7481
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SCO1 protein homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8423
Polymers18,7481
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.461, 52.444, 136.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe protein is monomeric in vivo but there are two molecules in the asymmetric unit.

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Components

#1: Protein SCO1 protein homolog, mitochondrial


Mass: 18748.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SCO1 / Production host: Escherichia coli (E. coli) / References: UniProt: O75880
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 Tris-HCl, 25% PEG6000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2005
Details: Channel-cut silicon monochromator and cylindrical grazing incidence mirror
RadiationMonochromator: Channel-cut silicon monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→78.2 Å / Num. all: 14686 / Num. obs: 14686 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 46.78 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 6.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 1.6 / Num. unique all: 5541 / Rsym value: 0.455 / % possible all: 81.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wp0

1wp0


Resolution: 2.4→36.74 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.869 / SU B: 10.831 / SU ML: 0.257 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.548 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31793 1328 9 %RANDOM
Rwork0.21673 ---
all0.22562 13358 --
obs0.22562 13358 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.56 Å2
Refine analyzeLuzzati sigma a obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 2.4→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2630 0 4 57 2691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0222698
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.921.983668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8535325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59624.264129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.6315453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2151515
X-RAY DIFFRACTIONr_chiral_restr0.2250.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022073
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2920.21292
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.330.21708
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1580.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0690.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5761.51705
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.58122662
X-RAY DIFFRACTIONr_scbond_it3.93131171
X-RAY DIFFRACTIONr_scangle_it5.4944.51006
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.397→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 77 -
Rwork0.247 724 -
obs--100 %

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