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- PDB-5vde: Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form I -

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Basic information

Entry
Database: PDB / ID: 5vde
TitleCrystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form I
ComponentsMetal homeostasis factor ATX1
KeywordsMETAL BINDING PROTEIN / Atx1 / metallochaperone / copper transfer / metal-binding domain / ferredoxin-like fold
Function / homology
Function and homology information


copper chaperone activity / copper ion transport / cellular response to oxidative stress / intracellular iron ion homeostasis / metal ion binding / cytosol
Similarity search - Function
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 ATX1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLee, M. / Maher, M.J.
CitationJournal: J. Inorg. Biochem. / Year: 2017
Title: The crystal structures of a copper-bound metallochaperone from Saccharomyces cerevisiae.
Authors: Lee, M. / Cooray, N.D.G. / Maher, M.J.
History
DepositionApr 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal homeostasis factor ATX1
B: Metal homeostasis factor ATX1
C: Metal homeostasis factor ATX1
D: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0586
Polymers32,9314
Non-polymers1272
Water4,107228
1
A: Metal homeostasis factor ATX1
B: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Metal homeostasis factor ATX1
D: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5293
Polymers16,4652
Non-polymers641
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Metal homeostasis factor ATX1
B: Metal homeostasis factor ATX1
hetero molecules

C: Metal homeostasis factor ATX1
D: Metal homeostasis factor ATX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0586
Polymers32,9314
Non-polymers1272
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area2940 Å2
ΔGint-35 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.976, 80.054, 50.763
Angle α, β, γ (deg.)90.00, 99.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Metal homeostasis factor ATX1


Mass: 8232.650 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ATX1, YNL259C, N0840 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38636
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1 M HEPES (pH 7.3), 24% (W/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 34104 / % possible obs: 97.3 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.057 / Net I/σ(I): 10.2
Reflection shellResolution: 1.65→1.7 Å / Redundancy: 4.7 % / Num. unique obs: 2129 / CC1/2: 0.748 / Rpim(I) all: 0.499 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CC8

1cc8


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.121 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.20589 1710 5.2 %RANDOM
Rwork0.16372 ---
obs0.16593 31480 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-1.44 Å2
2--0.28 Å20 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 2 228 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022336
X-RAY DIFFRACTIONr_bond_other_d0.0020.022337
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9953154
X-RAY DIFFRACTIONr_angle_other_deg1.02635484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.13126.27986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19315492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.744154
X-RAY DIFFRACTIONr_chiral_restr0.1250.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022473
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02395
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_it1.9041.6181154
X-RAY DIFFRACTIONr_mcbond_other1.8521.6141153
X-RAY DIFFRACTIONr_mcangle_it2.7372.4061441
X-RAY DIFFRACTIONr_mcangle_other2.7562.411442
X-RAY DIFFRACTIONr_scbond_it3.3452.1121182
X-RAY DIFFRACTIONr_scbond_other3.3382.1121182
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2462.9711702
X-RAY DIFFRACTIONr_long_range_B_refined6.88120.9612607
X-RAY DIFFRACTIONr_long_range_B_other6.79820.4592560
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 127 -
Rwork0.245 2129 -
obs--89.03 %

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