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- PDB-6ff1: CsoZ metallochaperone -

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Basic information

Entry
Database: PDB / ID: 6ff1
TitleCsoZ metallochaperone
ComponentsCsoZ
KeywordsCHAPERONE / metallochaperone / copper / copper homeostasis / staphylococcus aureus
Function / homologyHeavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy metal-associated domain, HMA / metal ion binding / HMA domain-containing protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsPelicioli-Riboldi, G. / Basle, A. / Waldron, K.
Funding support United Kingdom, Brazil, 2items
OrganizationGrant numberCountry
Sir Henry Dale Welcome and the Royal Society098375/Z/12/Z United Kingdom
CAPES Science without borders scholarshipBEX 2445/13-1 Brazil
CitationJournal: To Be Published
Title: The copper homeostasis system of Staphylococcus aureus: Two putative metallochaperones with contrasting copper binding properties.
Authors: Pelicioli-Riboldi, G. / Tarrant, E. / Basle, A. / Davies, O. / Waldron, K.
History
DepositionJan 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.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_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CsoZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8892
Polymers7,8491
Non-polymers401
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-5 kcal/mol
Surface area4410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.048, 51.048, 64.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CsoZ


Mass: 7848.718 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Strain: SH1000 / Gene: SAOUHSC_02321 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FWH0
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM CaCl2, 100 mM sodium acetate pH 5.0, 20%w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.3→44.21 Å / Num. obs: 24651 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.997 / Net I/σ(I): 10
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1184 / CC1/2: 0.868 / % possible all: 100

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Processing

Software
NameClassification
GDAdata collection
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
BUCCANEERmodel building
ARP/wARPmodel building
REFMACrefinement
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: SAD / Resolution: 1.3→44.21 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.625 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.039 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17217 1141 4.6 %RANDOM
Rwork0.14218 ---
obs0.14359 23478 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.051 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å2-0 Å2
2--0.12 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 1.3→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms550 0 1 121 672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019574
X-RAY DIFFRACTIONr_bond_other_d0.0030.02511
X-RAY DIFFRACTIONr_angle_refined_deg1.781.919782
X-RAY DIFFRACTIONr_angle_other_deg1.08631196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.027572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89426.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.75515102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.74151
X-RAY DIFFRACTIONr_chiral_restr0.1420.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02640
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02101
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_it1.4461.408282
X-RAY DIFFRACTIONr_mcbond_other1.4471.405281
X-RAY DIFFRACTIONr_mcangle_it1.672.123353
X-RAY DIFFRACTIONr_mcangle_other1.6682.124354
X-RAY DIFFRACTIONr_scbond_it4.5671.886292
X-RAY DIFFRACTIONr_scbond_other4.561.885293
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8822.657429
X-RAY DIFFRACTIONr_long_range_B_refined4.66120.243679
X-RAY DIFFRACTIONr_long_range_B_other4.11519.129653
X-RAY DIFFRACTIONr_rigid_bond_restr3.7131085
X-RAY DIFFRACTIONr_sphericity_free26.65578
X-RAY DIFFRACTIONr_sphericity_bonded10.08551119
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 79 -
Rwork0.261 1714 -
obs--100 %

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