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- PDB-3zk0: The crystal structure of a Cu(I) metallochaperone from Streptomyc... -

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Basic information

Entry
Database: PDB / ID: 3zk0
TitleThe crystal structure of a Cu(I) metallochaperone from Streptomyces lividans in its apo form
ComponentsSCO3965
KeywordsCHAPERONE / METALLOCHAPERONE
Function / homology
Function and homology information


PCu(A)C copper chaperone / Copper chaperone PCuAC / Copper chaperone PCuAC superfamily / Copper chaperone PCu(A)C / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Lipoprotein / Copper chaperone PCu(A)C
Similarity search - Component
Biological speciesSTREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBlundell, K.L.I.M. / Hough, M. / 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
DepositionJan 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SCO3965


Theoretical massNumber of molelcules
Total (without water)14,6671
Polymers14,6671
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.600, 47.680, 48.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SCO3965


Mass: 14667.101 Da / Num. of mol.: 1 / Fragment: RESIDUES 42-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93J41, UniProt: A0A7U9HCA5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFULL-LENGTH SEQUENCE IS 178 AMINO-ACIDS. N-TERMINAL TRANSMEMBRANE HELIX REMOVED, AND CONSTRUCT ...FULL-LENGTH SEQUENCE IS 178 AMINO-ACIDS. N-TERMINAL TRANSMEMBRANE HELIX REMOVED, AND CONSTRUCT CRYSTALLISED BEGINS AT SER-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: 1.57 Å3/Da / Density % sol: 21.8 % / Description: NONE
Crystal growDetails: 31 % PEG 8K, 0.2 M SODIUM ACETATE AND 0.1 M SODIUM CACODYLATE, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.2
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.7→34.16 Å / Num. obs: 11478 / % possible obs: 98 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.9 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZJA

3zja


Resolution: 1.7→34.16 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.386 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23303 544 4.8 %RANDOM
Rwork0.18323 ---
obs0.18561 10898 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.6 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2---1.34 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 0 0 82 948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.019937
X-RAY DIFFRACTIONr_bond_other_d0.0010.02885
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9611287
X-RAY DIFFRACTIONr_angle_other_deg0.80932061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4445136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57226.15439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79115158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.686152
X-RAY DIFFRACTIONr_chiral_restr0.10.2149
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 34 -
Rwork0.289 680 -
obs--85.1 %

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