[English] 日本語
Yorodumi
- PDB-2ggt: Crystal structure of human SCO1 complexed with nickel. -

+
Open data


ID or keywords:

Loading...

-
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 respiratory chain complex IV 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more