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- PDB-4bpy: Crystal structure of the C90A mutant of the Sco copper chaperone ... -

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Basic information

Entry
Database: PDB / ID: 4bpy
TitleCrystal structure of the C90A mutant of the Sco copper chaperone protein from Streptomyces lividans
ComponentsSCO PROTEIN
KeywordsCHAPERONE / COPPER HOMEOSTASIS / HOMEOSTASIS
Function / homology
Function and homology information


Copper chaperone SCO1/SenC / SCO1/SenC / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SCO1-SenC protein / Secreted protein
Similarity search - Component
Biological speciesSTREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBlundell, K.L.I.M. / Hough, M.A. / Worrall, J.A.R.
CitationJournal: Biochem.J. / Year: 2014
Title: Structural and Mechanistic Insights Into an Extracytoplasmic Copper Trafficking Pathway in Streptomyces Lividans.
Authors: Blundell, K.L.I.M. / Hough, M.A. / Vijgenboom, E. / Worrall, J.A.R.
History
DepositionMay 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SCO PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,0591
Polymers19,0591
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.200, 41.200, 76.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein SCO PROTEIN


Mass: 19059.484 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q93J40, UniProt: A0A7U9HC27*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTRUNCATED CONSTRUCT BEGINNING WITH RESIDUE 42

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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: 1.92 Å3/Da / Density % sol: 37.9 % / Description: NONE
Crystal growpH: 4.5 / Details: 28 % PEG 4000, 0.05 M NAAC PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2013 / Details: MIRRORS
RadiationMonochromator: SI DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→35.7 Å / Num. obs: 28622 / % possible obs: 99.8 % / Observed criterion σ(I): 100 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.1
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B7K

2b7k


Resolution: 1.4→35.68 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.564 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. ANISOTROPIC BS
RfactorNum. reflection% reflectionSelection details
Rfree0.18484 1441 5 %RANDOM
Rwork0.13075 ---
obs0.1335 27122 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.786 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20.6 Å20 Å2
2--0.6 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 1.4→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 0 121 1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021331
X-RAY DIFFRACTIONr_bond_other_d0.0010.021301
X-RAY DIFFRACTIONr_angle_refined_deg1.86321825
X-RAY DIFFRACTIONr_angle_other_deg1.19433031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49525.96252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.48715232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.253154
X-RAY DIFFRACTIONr_chiral_restr0.1130.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211499
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02259
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.73632632
X-RAY DIFFRACTIONr_sphericity_free32.005527
X-RAY DIFFRACTIONr_sphericity_bonded12.83252690
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 94 -
Rwork0.262 1973 -
obs--98.06 %

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