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- PDB-3i9z: Crystal structure of a metallochaperone with a trinuclear Cu(I) c... -

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Basic information

Entry
Database: PDB / ID: 3i9z
TitleCrystal structure of a metallochaperone with a trinuclear Cu(I) cluster
ComponentsCopper chaperone copZ
KeywordsCHAPERONE / Copper / Cytoplasm / Metal-binding
Function / homology
Function and homology information


copper ion transport / copper ion binding / cytoplasm
Similarity search - Function
: / Copper ion binding protein / Heavy metal-associated domain, copper ion-binding / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 ...: / Copper ion binding protein / Heavy metal-associated domain, copper ion-binding / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (I) ION / Copper chaperone CopZ
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHearnshaw, S.J. / Zhou, L. / Le Brun, N.E. / Hemmings, A.M.
CitationJournal: Biochem.J. / Year: 2009
Title: Mechanistic insights into Cu(I) cluster transfer between the chaperone CopZ and its cognate Cu(I)-transporting P-type ATPase, CopA.
Authors: Singleton, C. / Hearnshaw, S. / Zhou, L. / Le Brun, N.E. / Hemmings, A.M.
History
DepositionJul 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Copper chaperone copZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4102
Polymers7,3461
Non-polymers641
Water36020
1
A: Copper chaperone copZ
hetero molecules

A: Copper chaperone copZ
hetero molecules

A: Copper chaperone copZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2296
Polymers22,0393
Non-polymers1913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area2100 Å2
ΔGint-51.3 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.960, 63.960, 27.298
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-3005-

HOH

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Components

#1: Protein Copper chaperone copZ / Copper-ion-binding protein


Mass: 7346.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 1A1 / Gene: BSU33510, copZ, COPZ_BACSU, yvgY / Production host: Escherichia coli (E. coli) / Strain (production host): Jm109 / References: UniProt: O32221
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30 % w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.38 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2007
RadiationMonochromator: Double crystal Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 5023 / Num. obs: 5019 / % possible obs: 99.92 % / Observed criterion σ(I): 4 / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 29.1
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 8.6 / Num. unique all: 608 / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
MOLREPphasing
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→10 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 249 -RANDOM
Rwork0.1908 ---
obs0.1908 4978 99.18 %-
all-5019 --
Displacement parametersBiso mean: 17.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms506 0 1 20 527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.011
X-RAY DIFFRACTIONr_angle_refined_deg2
X-RAY DIFFRACTIONr_chiral_restr0.023
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 6 /
Rfactor% reflection
Rfree0.2702 -
Rwork0.1895 -
obs-87.23 %

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