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- PDB-1xzo: Identification of a disulfide switch in BsSco, a member of the Sc... -

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Basic information

Entry
Database: PDB / ID: 1xzo
TitleIdentification of a disulfide switch in BsSco, a member of the Sco family of cytochrome c oxidase assembly proteins
ComponentsHypothetical protein ypmQHypothesis
KeywordsMETAL BINDING PROTEIN / thioredoxin-like fold / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


metal ion binding / plasma membrane
Similarity search - Function
Copper chaperone SCO1/SenC / SCO1/SenC / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / SCO1 protein homolog
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.702 Å
AuthorsYe, Q. / Imriskova-Sosova, I. / Hill, B.C. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Biochemistry / Year: 2005
Title: Identification of a Disulfide Switch in BsSco, a Member of the Sco Family of Cytochrome c Oxidase Assembly Proteins
Authors: Ye, Q. / Imriskova-Sosova, I. / Hill, B.C. / Jia, Z.
History
DepositionNov 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 2.0Jun 17, 2020Group: Database references / Polymer sequence
Category: entity_poly / pdbx_database_related / struct_ref_seq_dif
Item: _entity_poly.pdbx_target_identifier / _struct_ref_seq_dif.details
Revision 2.1Feb 14, 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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: Hypothetical protein ypmQ
B: Hypothetical protein ypmQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,61321
Polymers39,4902
Non-polymers1,12319
Water6,990388
1
A: Hypothetical protein ypmQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,51513
Polymers19,7451
Non-polymers77012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein ypmQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0988
Polymers19,7451
Non-polymers3537
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hypothetical protein ypmQ
B: Hypothetical protein ypmQ
hetero molecules

A: Hypothetical protein ypmQ
B: Hypothetical protein ypmQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,22742
Polymers78,9804
Non-polymers2,24638
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7190 Å2
ΔGint-338 kcal/mol
Surface area33120 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.033, 68.033, 191.733
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Hypothetical protein ypmQ / Hypothesis / BSSCO


Mass: 19745.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: DH5f / Gene: ypmQ / Plasmid: PNM137 / Production host: Escherichia coli (E. coli) / References: UniProt: P54178
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 3.12 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG5K MME, CdCl2, CaCl2, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 27, 2003
RadiationMonochromator: Si(III) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.7→64.55 Å / Num. all: 57817 / Num. obs: 54348 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.7→1.76 Å / % possible all: 0.94

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.702→37.2 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.079 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28935 2771 5.1 %RANDOM
Rwork0.23824 ---
obs0.24088 51554 94.6 %-
all-57817 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.669 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.17 Å20 Å2
2--0.35 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.702→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 19 388 3128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0222767
X-RAY DIFFRACTIONr_bond_other_d0.0030.022347
X-RAY DIFFRACTIONr_angle_refined_deg2.3881.9563737
X-RAY DIFFRACTIONr_angle_other_deg1.14735523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7485336
X-RAY DIFFRACTIONr_chiral_restr0.1620.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023052
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02510
X-RAY DIFFRACTIONr_nbd_refined0.3310.2871
X-RAY DIFFRACTIONr_nbd_other0.2710.22856
X-RAY DIFFRACTIONr_nbtor_other0.0960.21609
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3150.2316
X-RAY DIFFRACTIONr_metal_ion_refined0.5150.228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3630.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.270.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5060.229
X-RAY DIFFRACTIONr_mcbond_it1.6181.51708
X-RAY DIFFRACTIONr_mcangle_it2.70822764
X-RAY DIFFRACTIONr_scbond_it4.00931059
X-RAY DIFFRACTIONr_scangle_it5.9224.5973
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.355 129
Rwork0.292 2450

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